From 4c5973f8125cdf68b3ca7eae47ec968578db0538 Mon Sep 17 00:00:00 2001 From: robert-a-forsyth Date: Thu, 30 Oct 2025 17:02:21 +0100 Subject: [PATCH 01/42] fix clairs indel calling --- modules/local/clairs/main.nf | 6 +++++- modules/nf-core/ensemblvep/vep/main.nf | 2 +- subworkflows/local/tumor_normal_happhase.nf | 2 +- tests/default.nf.test.snap | 12 ++++++++++-- 4 files changed, 17 insertions(+), 5 deletions(-) diff --git a/modules/local/clairs/main.nf b/modules/local/clairs/main.nf index 5d710693..f727c214 100644 --- a/modules/local/clairs/main.nf +++ b/modules/local/clairs/main.nf @@ -12,7 +12,9 @@ process CLAIRS { tuple val(meta3), path(index) output: - tuple val(meta), path("*.vcf.gz"), emit: vcf + tuple val(meta), path("${meta.id}.vcf.gz"), emit: all_vcf + tuple val(meta), path("indel.vcf.gz"), emit: indel_vcf + tuple val(meta), path("snv.vcf.gz"), emit: snv_vcf tuple val(meta), path("*.vcf.gz.tbi"), emit: tbi path "versions.yml", emit: versions @@ -29,6 +31,8 @@ process CLAIRS { --normal_bam_fn $normal_bam \\ --ref_fn $reference \\ --threads $task.cpus \\ + --enable_indel_calling \\ + --haplotagged_tumor_bam_provided_so_skip_intermediate_phasing_and_haplotagging \\ --platform $model \\ --output_dir . \\ --output_prefix $prefix \\ diff --git a/modules/nf-core/ensemblvep/vep/main.nf b/modules/nf-core/ensemblvep/vep/main.nf index 80c91f0d..6ef37082 100644 --- a/modules/nf-core/ensemblvep/vep/main.nf +++ b/modules/nf-core/ensemblvep/vep/main.nf @@ -1,6 +1,6 @@ process ENSEMBLVEP_VEP { tag "${meta.id}" - label 'process_medium' + label 'process_very_high' conda "${moduleDir}/environment.yml" container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container diff --git a/subworkflows/local/tumor_normal_happhase.nf b/subworkflows/local/tumor_normal_happhase.nf index fd6ed3c0..cf998016 100644 --- a/subworkflows/local/tumor_normal_happhase.nf +++ b/subworkflows/local/tumor_normal_happhase.nf @@ -268,7 +268,7 @@ workflow TUMOR_NORMAL_HAPPHASE { fai ) - CLAIRS.out.vcf + CLAIRS.out.all_vcf .map { meta, vcf -> def extra = [] return [meta,vcf, extra] diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index e15225dc..64647d66 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -148,8 +148,12 @@ "sample1/variants/clair3/merge_output.vcf.gz", "sample1/variants/clair3/merge_output.vcf.gz.tbi", "sample1/variants/clairs", + "sample1/variants/clairs/indel.vcf.gz", + "sample1/variants/clairs/indel.vcf.gz.tbi", "sample1/variants/clairs/sample1.vcf.gz", "sample1/variants/clairs/sample1.vcf.gz.tbi", + "sample1/variants/clairs/snv.vcf.gz", + "sample1/variants/clairs/snv.vcf.gz.tbi", "sample1/variants/severus", "sample1/variants/severus/all_SVs", "sample1/variants/severus/all_SVs/breakpoint_clusters.tsv", @@ -214,8 +218,12 @@ "sample2/variants/clair3/merge_output.vcf.gz", "sample2/variants/clair3/merge_output.vcf.gz.tbi", "sample2/variants/clairs", + "sample2/variants/clairs/indel.vcf.gz", + "sample2/variants/clairs/indel.vcf.gz.tbi", "sample2/variants/clairs/sample2.vcf.gz", "sample2/variants/clairs/sample2.vcf.gz.tbi", + "sample2/variants/clairs/snv.vcf.gz", + "sample2/variants/clairs/snv.vcf.gz.tbi", "sample2/variants/severus", "sample2/variants/severus/all_SVs", "sample2/variants/severus/all_SVs/breakpoint_clusters.tsv", @@ -358,8 +366,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "25.09.0" + "nextflow": "25.04.6" }, - "timestamp": "2025-10-09T12:54:36.36718409" + "timestamp": "2025-10-30T17:00:44.230935974" } } \ No newline at end of file From d60b5eea79a8311f608b38a8dac6a02e3dde4c9f Mon Sep 17 00:00:00 2001 From: robert-a-forsyth Date: Tue, 18 Nov 2025 11:34:36 +0100 Subject: [PATCH 02/42] view --- conf/modules.config | 8 ++------ modules/local/clairs/main.nf | 8 ++++---- modules/local/metaextract/main.nf | 4 ++-- subworkflows/local/prepare_reference_files.nf | 2 ++ .../local/utils_nfcore_lrsomatic_pipeline/main.nf | 2 ++ 5 files changed, 12 insertions(+), 12 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 9cd2e5a7..2e86eb6d 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -168,18 +168,14 @@ process { ].join(' ').trim() } publishDir = [ - path: { "${params.outdir}/${meta.id}/methylation/${meta.type}/fibertoolsrs/predictm6a" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + enabled: false ] } withName: '.*:FIBERTOOLSRS_FIRE' { ext.args = { (meta.platform == "ont") ? "--ont" : "" } publishDir = [ - path: { "${params.outdir}/${meta.id}/methylation/${meta.type}/fibertoolsrs/fire" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + enabled: false ] } diff --git a/modules/local/clairs/main.nf b/modules/local/clairs/main.nf index f727c214..065eb46c 100644 --- a/modules/local/clairs/main.nf +++ b/modules/local/clairs/main.nf @@ -13,10 +13,10 @@ process CLAIRS { output: tuple val(meta), path("${meta.id}.vcf.gz"), emit: all_vcf - tuple val(meta), path("indel.vcf.gz"), emit: indel_vcf - tuple val(meta), path("snv.vcf.gz"), emit: snv_vcf - tuple val(meta), path("*.vcf.gz.tbi"), emit: tbi - path "versions.yml", emit: versions + tuple val(meta), path("indel.vcf.gz"), emit: indel_vcf + tuple val(meta), path("snv.vcf.gz"), emit: snv_vcf + tuple val(meta), path("*.vcf.gz.tbi"), emit: tbi + path "versions.yml", emit: versions when: task.ext.when == null || task.ext.when diff --git a/modules/local/metaextract/main.nf b/modules/local/metaextract/main.nf index 48d75ed1..7f032250 100644 --- a/modules/local/metaextract/main.nf +++ b/modules/local/metaextract/main.nf @@ -11,8 +11,8 @@ process METAEXTRACT { tuple val(meta), path(bam) output: - tuple val(meta), env(basecall_model),env(kinetics) , emit: meta_ext - path "versions.yml" , emit: versions + tuple val(meta), env(basecall_model), env(kinetics) , emit: meta_ext + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when diff --git a/subworkflows/local/prepare_reference_files.nf b/subworkflows/local/prepare_reference_files.nf index fa5da439..a7d94704 100644 --- a/subworkflows/local/prepare_reference_files.nf +++ b/subworkflows/local/prepare_reference_files.nf @@ -39,6 +39,7 @@ workflow PREPARE_REFERENCE_FILES { ch_prepared_fasta = [ [:], fasta ] } + basecall_meta.view() basecall_meta.map { meta, basecall_model_meta, kinetics_meta -> def meta_new = [id: basecall_model_meta] @@ -50,6 +51,7 @@ workflow PREPARE_REFERENCE_FILES { .unique() .set{ model_urls } + model_urls.view() // // MODULE: Download model diff --git a/subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf b/subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf index 60e847cc..788af9c9 100644 --- a/subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf @@ -100,6 +100,8 @@ workflow PIPELINE_INITIALISATION { } .set { ch_samplesheet } + ch_samplesheet.view() + // ch_samplesheet -> meta: [id, paired_data, platform, sex, type] // bam: unaligned bams From b20166fa374a51c012323c15377dce6625d54092 Mon Sep 17 00:00:00 2001 From: robert-a-forsyth Date: Tue, 18 Nov 2025 14:24:52 +0100 Subject: [PATCH 03/42] fix id --- subworkflows/local/prepare_reference_files.nf | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/subworkflows/local/prepare_reference_files.nf b/subworkflows/local/prepare_reference_files.nf index a7d94704..36fcada3 100644 --- a/subworkflows/local/prepare_reference_files.nf +++ b/subworkflows/local/prepare_reference_files.nf @@ -42,7 +42,8 @@ workflow PREPARE_REFERENCE_FILES { basecall_meta.view() basecall_meta.map { meta, basecall_model_meta, kinetics_meta -> - def meta_new = [id: basecall_model_meta] + def id_new = basecall_model_meta ?: meta.clair3_model + def meta_new = [id: id_new] def model = (!meta.clair3_model || meta.clair3_model.toString().trim() in ['', '[]']) ? clair3_modelMap.get(basecall_model_meta) : meta.clair3_model def download_prefix = ( basecall_model_meta == 'hifi_revio' ? "https://www.bio8.cs.hku.hk/clair3/clair3_models/" : "https://cdn.oxfordnanoportal.com/software/analysis/models/clair3" ) def url = "${download_prefix}/${model}.tar.gz" From 233059acedd585494a39b76c7726c215b7f750d9 Mon Sep 17 00:00:00 2001 From: robert-a-forsyth Date: Tue, 18 Nov 2025 14:36:05 +0100 Subject: [PATCH 04/42] remove view --- subworkflows/local/prepare_reference_files.nf | 2 -- subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf | 1 - workflows/lrsomatic.nf | 5 ----- 3 files changed, 8 deletions(-) diff --git a/subworkflows/local/prepare_reference_files.nf b/subworkflows/local/prepare_reference_files.nf index 36fcada3..722b9f73 100644 --- a/subworkflows/local/prepare_reference_files.nf +++ b/subworkflows/local/prepare_reference_files.nf @@ -39,7 +39,6 @@ workflow PREPARE_REFERENCE_FILES { ch_prepared_fasta = [ [:], fasta ] } - basecall_meta.view() basecall_meta.map { meta, basecall_model_meta, kinetics_meta -> def id_new = basecall_model_meta ?: meta.clair3_model @@ -52,7 +51,6 @@ workflow PREPARE_REFERENCE_FILES { .unique() .set{ model_urls } - model_urls.view() // // MODULE: Download model diff --git a/subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf b/subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf index 788af9c9..91915a3e 100644 --- a/subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf @@ -100,7 +100,6 @@ workflow PIPELINE_INITIALISATION { } .set { ch_samplesheet } - ch_samplesheet.view() // ch_samplesheet -> meta: [id, paired_data, platform, sex, type] // bam: unaligned bams diff --git a/workflows/lrsomatic.nf b/workflows/lrsomatic.nf index 5ff7997d..2b84c973 100644 --- a/workflows/lrsomatic.nf +++ b/workflows/lrsomatic.nf @@ -218,7 +218,6 @@ workflow LRSOMATIC { // predict m6a in unaligned bam if (!params.skip_fiber) { - //ch_cat_ubams.view() if(!params.normal_fiber){ ch_cat_ubams .branch { meta, bams -> @@ -228,9 +227,7 @@ workflow LRSOMATIC { .set { ch_cat_ubams_normal_branching } normal_bams = ch_cat_ubams_normal_branching.normal - normal_bams.view() ubams = ch_cat_ubams_normal_branching.tumor - ubams.view() } else { ubams = ch_cat_ubams @@ -243,7 +240,6 @@ workflow LRSOMATIC { .set{ch_cat_ubams_pacbio_ont_branching} pacbio_bams = ch_cat_ubams_pacbio_ont_branching.pacBio - pacbio_bams.view() pacbio_bams .branch{meta, bams -> kinetics: meta.kinetics == "true" @@ -295,7 +291,6 @@ workflow LRSOMATIC { fiber_branch.nonFiber .mix(normal_bams) .mix(FIBERTOOLSRS_FIRE.out.bam) - .view() .set{ch_cat_ubams} } From 4350f5743ea22f2da535d7b7d502b46e2c681feb Mon Sep 17 00:00:00 2001 From: robert-a-forsyth Date: Tue, 18 Nov 2025 19:09:05 +0100 Subject: [PATCH 05/42] Revert "fix id" This reverts commit b20166fa374a51c012323c15377dce6625d54092. --- subworkflows/local/prepare_reference_files.nf | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/subworkflows/local/prepare_reference_files.nf b/subworkflows/local/prepare_reference_files.nf index 722b9f73..fa5da439 100644 --- a/subworkflows/local/prepare_reference_files.nf +++ b/subworkflows/local/prepare_reference_files.nf @@ -41,8 +41,7 @@ workflow PREPARE_REFERENCE_FILES { basecall_meta.map { meta, basecall_model_meta, kinetics_meta -> - def id_new = basecall_model_meta ?: meta.clair3_model - def meta_new = [id: id_new] + def meta_new = [id: basecall_model_meta] def model = (!meta.clair3_model || meta.clair3_model.toString().trim() in ['', '[]']) ? clair3_modelMap.get(basecall_model_meta) : meta.clair3_model def download_prefix = ( basecall_model_meta == 'hifi_revio' ? "https://www.bio8.cs.hku.hk/clair3/clair3_models/" : "https://cdn.oxfordnanoportal.com/software/analysis/models/clair3" ) def url = "${download_prefix}/${model}.tar.gz" From d3623ac99fc88573fb3fbb9ca304b80061ac91ad Mon Sep 17 00:00:00 2001 From: robert-a-forsyth Date: Tue, 18 Nov 2025 19:11:00 +0100 Subject: [PATCH 06/42] revert --- subworkflows/local/prepare_reference_files.nf | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/subworkflows/local/prepare_reference_files.nf b/subworkflows/local/prepare_reference_files.nf index fa5da439..722b9f73 100644 --- a/subworkflows/local/prepare_reference_files.nf +++ b/subworkflows/local/prepare_reference_files.nf @@ -41,7 +41,8 @@ workflow PREPARE_REFERENCE_FILES { basecall_meta.map { meta, basecall_model_meta, kinetics_meta -> - def meta_new = [id: basecall_model_meta] + def id_new = basecall_model_meta ?: meta.clair3_model + def meta_new = [id: id_new] def model = (!meta.clair3_model || meta.clair3_model.toString().trim() in ['', '[]']) ? clair3_modelMap.get(basecall_model_meta) : meta.clair3_model def download_prefix = ( basecall_model_meta == 'hifi_revio' ? "https://www.bio8.cs.hku.hk/clair3/clair3_models/" : "https://cdn.oxfordnanoportal.com/software/analysis/models/clair3" ) def url = "${download_prefix}/${model}.tar.gz" From 424befd3e01577006cbc8414cef84424986d8eaa Mon Sep 17 00:00:00 2001 From: robert-a-forsyth Date: Tue, 18 Nov 2025 19:17:38 +0100 Subject: [PATCH 07/42] patch --- modules.json | 102 +++++++++++++----- .../ensemblvep/vep/ensemblvep-vep.diff | 8 ++ 2 files changed, 84 insertions(+), 26 deletions(-) diff --git a/modules.json b/modules.json index 52190c75..dd0d6c88 100644 --- a/modules.json +++ b/modules.json @@ -8,113 +8,155 @@ "ascat": { "branch": "master", "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", - "installed_by": ["modules"], + "installed_by": [ + "modules" + ], "patch": "modules/nf-core/ascat/ascat.diff" }, "ensemblvep/download": { "branch": "master", "git_sha": "2fcc53751152a999bfc9c24f75f494b9e5bb338f", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "ensemblvep/vep": { "branch": "master", "git_sha": "48ca3de1737b0144aa9fe05bea2b681f0ae45a95", - "installed_by": ["modules"], + "installed_by": [ + "modules" + ], "patch": "modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff" }, "longphase/haplotag": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "longphase/phase": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"], + "installed_by": [ + "modules" + ], "patch": "modules/nf-core/longphase/phase/longphase-phase.diff" }, "minimap2/align": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"], + "installed_by": [ + "modules" + ], "patch": "modules/nf-core/minimap2/align/minimap2-align.diff" }, "minimap2/index": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "modkit/pileup": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "mosdepth": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "multiqc": { "branch": "master", "git_sha": "a4488d3d09244f29fb4606ba4eef85d59dcc6ad8", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "pigz/uncompress": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/cat": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/faidx": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/flagstat": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["bam_stats_samtools"] + "installed_by": [ + "bam_stats_samtools" + ] }, "samtools/idxstats": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["bam_stats_samtools"] + "installed_by": [ + "bam_stats_samtools" + ] }, "samtools/index": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/stats": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["bam_stats_samtools"], + "installed_by": [ + "bam_stats_samtools" + ], "patch": "modules/nf-core/samtools/stats/samtools-stats.diff" }, "severus": { "branch": "master", "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", - "installed_by": ["modules"], + "installed_by": [ + "modules" + ], "patch": "modules/nf-core/severus/severus.diff" }, "untar": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "unzip": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "wget": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] } } }, @@ -123,25 +165,33 @@ "bam_stats_samtools": { "branch": "master", "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nextflow_pipeline": { "branch": "master", "git_sha": "c2b22d85f30a706a3073387f30380704fcae013b", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "51ae5406a030d4da1e49e4dab49756844fdd6c7a", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nfschema_plugin": { "branch": "master", "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] } } } } } -} +} \ No newline at end of file diff --git a/modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff b/modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff index 3104732a..71c05d4b 100644 --- a/modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff +++ b/modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff @@ -3,6 +3,14 @@ Changes in component 'nf-core/ensemblvep/vep' Changes in 'ensemblvep/vep/main.nf': --- modules/nf-core/ensemblvep/vep/main.nf +++ modules/nf-core/ensemblvep/vep/main.nf +@@ -1,6 +1,6 @@ + process ENSEMBLVEP_VEP { + tag "${meta.id}" +- label 'process_medium' ++ label 'process_very_high' + + conda "${moduleDir}/environment.yml" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container @@ -15,6 +15,8 @@ path cache tuple val(meta2), path(fasta) From c70e403f5ae98ff1442953419995878ffabd0b2a Mon Sep 17 00:00:00 2001 From: robert-a-forsyth Date: Tue, 18 Nov 2025 19:18:42 +0100 Subject: [PATCH 08/42] prettier --- modules.json | 102 +++++++++++++-------------------------------------- 1 file changed, 26 insertions(+), 76 deletions(-) diff --git a/modules.json b/modules.json index dd0d6c88..52190c75 100644 --- a/modules.json +++ b/modules.json @@ -8,155 +8,113 @@ "ascat": { "branch": "master", "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/ascat/ascat.diff" }, "ensemblvep/download": { "branch": "master", "git_sha": "2fcc53751152a999bfc9c24f75f494b9e5bb338f", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "ensemblvep/vep": { "branch": "master", "git_sha": "48ca3de1737b0144aa9fe05bea2b681f0ae45a95", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff" }, "longphase/haplotag": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "longphase/phase": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/longphase/phase/longphase-phase.diff" }, "minimap2/align": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/minimap2/align/minimap2-align.diff" }, "minimap2/index": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "modkit/pileup": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "mosdepth": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "multiqc": { "branch": "master", "git_sha": "a4488d3d09244f29fb4606ba4eef85d59dcc6ad8", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "pigz/uncompress": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/cat": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/faidx": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/flagstat": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "bam_stats_samtools" - ] + "installed_by": ["bam_stats_samtools"] }, "samtools/idxstats": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "bam_stats_samtools" - ] + "installed_by": ["bam_stats_samtools"] }, "samtools/index": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/stats": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "bam_stats_samtools" - ], + "installed_by": ["bam_stats_samtools"], "patch": "modules/nf-core/samtools/stats/samtools-stats.diff" }, "severus": { "branch": "master", "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/severus/severus.diff" }, "untar": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "unzip": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "wget": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] } } }, @@ -165,33 +123,25 @@ "bam_stats_samtools": { "branch": "master", "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nextflow_pipeline": { "branch": "master", "git_sha": "c2b22d85f30a706a3073387f30380704fcae013b", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "51ae5406a030d4da1e49e4dab49756844fdd6c7a", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfschema_plugin": { "branch": "master", "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] } } } } } -} \ No newline at end of file +} From dadd850e1536553dd28a7848660bf2a089ca61a2 Mon Sep 17 00:00:00 2001 From: robert-a-forsyth Date: Wed, 19 Nov 2025 10:46:55 +0100 Subject: [PATCH 09/42] view --- conf/modules.config | 7 +++++++ subworkflows/local/tumor_normal_happhase.nf | 2 ++ 2 files changed, 9 insertions(+) diff --git a/conf/modules.config b/conf/modules.config index 2e86eb6d..a119e03f 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -179,6 +179,13 @@ process { ] } + withName: '.*:FIBERTOOLSRS_NUCLEOSOMES' { + ext.args = { (meta.platform == "ont") ? "--ont" : "" } + publishDir = [ + enabled: false + ] + } + // // Phasing processes // diff --git a/subworkflows/local/tumor_normal_happhase.nf b/subworkflows/local/tumor_normal_happhase.nf index cf998016..1c0bf976 100644 --- a/subworkflows/local/tumor_normal_happhase.nf +++ b/subworkflows/local/tumor_normal_happhase.nf @@ -220,6 +220,8 @@ workflow TUMOR_NORMAL_HAPPHASE { // bais: indexes for bam files // Group everything back together in one channel + mixed_hapbams.view() + mixed_hapbams .map { meta, bam, bai, vcf, snvs, mods, hapbam, hapbai -> def new_meta = [id: meta.id, From e45936715c37a29f796811f31fccd948981da481 Mon Sep 17 00:00:00 2001 From: robert-a-forsyth Date: Wed, 19 Nov 2025 11:11:05 +0100 Subject: [PATCH 10/42] grouptuple fix --- subworkflows/local/tumor_normal_happhase.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/tumor_normal_happhase.nf b/subworkflows/local/tumor_normal_happhase.nf index 1c0bf976..22e6714b 100644 --- a/subworkflows/local/tumor_normal_happhase.nf +++ b/subworkflows/local/tumor_normal_happhase.nf @@ -221,7 +221,7 @@ workflow TUMOR_NORMAL_HAPPHASE { // Group everything back together in one channel mixed_hapbams.view() - + mixed_hapbams .map { meta, bam, bai, vcf, snvs, mods, hapbam, hapbai -> def new_meta = [id: meta.id, @@ -232,7 +232,7 @@ workflow TUMOR_NORMAL_HAPPHASE { basecall_model: meta.basecall_model] return[new_meta, [[type: meta.type], hapbam], [[type: meta.type], hapbai]] } - .groupTuple() + .groupTuple(size: 2) .map{ meta, bam, bai -> def normal_bam = bam[0][0].type == "normal" ? bam[0][1] : bam[1][1] def tumor_bam = bam[0][0].type == "tumor" ? bam[0][1] : bam[1][1] From 678dc48c8460852c532f5f4868a3d80aeef46a82 Mon Sep 17 00:00:00 2001 From: robert-a-forsyth Date: Wed, 19 Nov 2025 13:47:33 +0100 Subject: [PATCH 11/42] remove nucleo arg --- conf/modules.config | 1 - 1 file changed, 1 deletion(-) diff --git a/conf/modules.config b/conf/modules.config index a119e03f..95d310d6 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -180,7 +180,6 @@ process { } withName: '.*:FIBERTOOLSRS_NUCLEOSOMES' { - ext.args = { (meta.platform == "ont") ? "--ont" : "" } publishDir = [ enabled: false ] From eaf4cae1e8cb2263b223db8aa65c0e38e5962740 Mon Sep 17 00:00:00 2001 From: ljwharbers Date: Thu, 20 Nov 2025 18:17:51 +0100 Subject: [PATCH 12/42] change meta.id to prefix in CLAIRS` --- modules/local/clairs/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/local/clairs/main.nf b/modules/local/clairs/main.nf index 065eb46c..99857f89 100644 --- a/modules/local/clairs/main.nf +++ b/modules/local/clairs/main.nf @@ -12,7 +12,7 @@ process CLAIRS { tuple val(meta3), path(index) output: - tuple val(meta), path("${meta.id}.vcf.gz"), emit: all_vcf + tuple val(meta), path("${prefix}.vcf.gz"), emit: all_vcf tuple val(meta), path("indel.vcf.gz"), emit: indel_vcf tuple val(meta), path("snv.vcf.gz"), emit: snv_vcf tuple val(meta), path("*.vcf.gz.tbi"), emit: tbi @@ -23,7 +23,7 @@ process CLAIRS { script: def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" + prefix = task.ext.prefix ?: "${meta.id}" """ /opt/bin/run_clairs \ From 49d337e6480e0aa68136374ff6562b1b83d35c16 Mon Sep 17 00:00:00 2001 From: ljwharbers Date: Thu, 20 Nov 2025 18:19:15 +0100 Subject: [PATCH 13/42] indentation --- modules/local/clairs/main.nf | 2 +- modules/nf-core/ensemblvep/vep/main.nf | 12 ++++++------ 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/modules/local/clairs/main.nf b/modules/local/clairs/main.nf index 99857f89..e7744781 100644 --- a/modules/local/clairs/main.nf +++ b/modules/local/clairs/main.nf @@ -12,7 +12,7 @@ process CLAIRS { tuple val(meta3), path(index) output: - tuple val(meta), path("${prefix}.vcf.gz"), emit: all_vcf + tuple val(meta), path("${prefix}.vcf.gz"), emit: all_vcf tuple val(meta), path("indel.vcf.gz"), emit: indel_vcf tuple val(meta), path("snv.vcf.gz"), emit: snv_vcf tuple val(meta), path("*.vcf.gz.tbi"), emit: tbi diff --git a/modules/nf-core/ensemblvep/vep/main.nf b/modules/nf-core/ensemblvep/vep/main.nf index 6ef37082..9daaadab 100644 --- a/modules/nf-core/ensemblvep/vep/main.nf +++ b/modules/nf-core/ensemblvep/vep/main.nf @@ -19,12 +19,12 @@ process ENSEMBLVEP_VEP { path custom_vep_tbi output: - tuple val(meta), path("*.vcf.gz"), emit: vcf, optional: true - tuple val(meta), path("*.vcf.gz.tbi"), emit: tbi, optional: true - tuple val(meta), path("*.tab.gz"), emit: tab, optional: true - tuple val(meta), path("*.json.gz"), emit: json, optional: true - path "*.html", emit: report, optional: true - path "versions.yml", emit: versions + tuple val(meta), path("*.vcf.gz"), emit: vcf, optional: true + tuple val(meta), path("*.vcf.gz.tbi"), emit: tbi, optional: true + tuple val(meta), path("*.tab.gz"), emit: tab, optional: true + tuple val(meta), path("*.json.gz"), emit: json, optional: true + path "*.html", emit: report, optional: true + path "versions.yml", emit: versions when: task.ext.when == null || task.ext.when From 484a09110a579faa303547d7153f252a081db09a Mon Sep 17 00:00:00 2001 From: ljwharbers Date: Thu, 20 Nov 2025 18:20:05 +0100 Subject: [PATCH 14/42] remove view statement --- subworkflows/local/tumor_normal_happhase.nf | 2 -- 1 file changed, 2 deletions(-) diff --git a/subworkflows/local/tumor_normal_happhase.nf b/subworkflows/local/tumor_normal_happhase.nf index 22e6714b..3d9635ac 100644 --- a/subworkflows/local/tumor_normal_happhase.nf +++ b/subworkflows/local/tumor_normal_happhase.nf @@ -220,8 +220,6 @@ workflow TUMOR_NORMAL_HAPPHASE { // bais: indexes for bam files // Group everything back together in one channel - mixed_hapbams.view() - mixed_hapbams .map { meta, bam, bai, vcf, snvs, mods, hapbam, hapbai -> def new_meta = [id: meta.id, From 200b95f41cd195cc0a93cd64086c46acb2d215ba Mon Sep 17 00:00:00 2001 From: robert-a-forsyth Date: Mon, 24 Nov 2025 09:54:28 +0100 Subject: [PATCH 15/42] add view --- subworkflows/local/tumor_only_happhase.nf | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/subworkflows/local/tumor_only_happhase.nf b/subworkflows/local/tumor_only_happhase.nf index 220a8710..644f5aac 100644 --- a/subworkflows/local/tumor_only_happhase.nf +++ b/subworkflows/local/tumor_only_happhase.nf @@ -22,7 +22,7 @@ workflow TUMOR_ONLY_HAPPHASE { tumor_only_severus = Channel.empty() somatic_vep = Channel.empty() germline_vep = Channel.empty() - + tumor_bams.view() tumor_bams .map{ meta, bam, bai -> def clairSTO_model = (!meta.clairSTO_model || meta.clairSTO_model.toString().trim() in ['', '[]']) ? clairSTO_modelMap.get(meta.basecall_model.toString().trim()) : meta.clairSTO_model @@ -30,6 +30,8 @@ workflow TUMOR_ONLY_HAPPHASE { } .set{ tumor_bams } + tumor_bams.view() + // // MODULE: CLAIRSTO // From 550ba65ea05aac00e4f143ebcf5efbdbf305d694 Mon Sep 17 00:00:00 2001 From: robert-a-forsyth Date: Mon, 24 Nov 2025 10:01:32 +0100 Subject: [PATCH 16/42] fix read-in --- subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf b/subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf index 91915a3e..7cd833a4 100644 --- a/subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf @@ -76,7 +76,7 @@ workflow PIPELINE_INITIALISATION { .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json")) .map { meta, bam_tumor, bam_normal, method, sex, fiber, clair3_model, clairSTO_model, clairS_model -> def real_clair3_model = (clair3_model == null ) ? null : clair3_model - def real_clairS_model = (clair3_model == null ) ? null : clairSTO_model + def real_clairS_model = (clair3_model == null ) ? null : clairS_model def real_clairSTO_model = (clair3_model == null ) ? null : clairS_model def paired_data = bam_normal ? true : false def meta_info = meta + [ paired_data: paired_data, platform: method, sex: sex, fiber: fiber, clair3_model: real_clair3_model, clairS_model : real_clairS_model, clairSTO_model: real_clairSTO_model] From afbb03a15ac22884a50fb3ea0fdadd974a81eaa6 Mon Sep 17 00:00:00 2001 From: robert-a-forsyth Date: Mon, 24 Nov 2025 10:06:35 +0100 Subject: [PATCH 17/42] fix read-in --- subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf b/subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf index 7cd833a4..6db20132 100644 --- a/subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf @@ -77,7 +77,7 @@ workflow PIPELINE_INITIALISATION { .map { meta, bam_tumor, bam_normal, method, sex, fiber, clair3_model, clairSTO_model, clairS_model -> def real_clair3_model = (clair3_model == null ) ? null : clair3_model def real_clairS_model = (clair3_model == null ) ? null : clairS_model - def real_clairSTO_model = (clair3_model == null ) ? null : clairS_model + def real_clairSTO_model = (clair3_model == null ) ? null : real_clairSTO_model def paired_data = bam_normal ? true : false def meta_info = meta + [ paired_data: paired_data, platform: method, sex: sex, fiber: fiber, clair3_model: real_clair3_model, clairS_model : real_clairS_model, clairSTO_model: real_clairSTO_model] return [ meta_info, [ bam_tumor ], [ bam_normal ?: [] ] ] From ec83c21dfd65ad226bbccd0072cdf870987d2136 Mon Sep 17 00:00:00 2001 From: robert-a-forsyth Date: Mon, 24 Nov 2025 10:44:15 +0100 Subject: [PATCH 18/42] fix read-in --- subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf b/subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf index 6db20132..58508b54 100644 --- a/subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf @@ -77,7 +77,7 @@ workflow PIPELINE_INITIALISATION { .map { meta, bam_tumor, bam_normal, method, sex, fiber, clair3_model, clairSTO_model, clairS_model -> def real_clair3_model = (clair3_model == null ) ? null : clair3_model def real_clairS_model = (clair3_model == null ) ? null : clairS_model - def real_clairSTO_model = (clair3_model == null ) ? null : real_clairSTO_model + def real_clairSTO_model = (clair3_model == null ) ? null : clairSTO_model def paired_data = bam_normal ? true : false def meta_info = meta + [ paired_data: paired_data, platform: method, sex: sex, fiber: fiber, clair3_model: real_clair3_model, clairS_model : real_clairS_model, clairSTO_model: real_clairSTO_model] return [ meta_info, [ bam_tumor ], [ bam_normal ?: [] ] ] From 339449aaa056b78c46bbdde8beba1f7ac6b86276 Mon Sep 17 00:00:00 2001 From: robert-a-forsyth Date: Mon, 24 Nov 2025 10:52:09 +0100 Subject: [PATCH 19/42] fix read-in --- subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf b/subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf index 58508b54..a9266bed 100644 --- a/subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf @@ -76,8 +76,8 @@ workflow PIPELINE_INITIALISATION { .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json")) .map { meta, bam_tumor, bam_normal, method, sex, fiber, clair3_model, clairSTO_model, clairS_model -> def real_clair3_model = (clair3_model == null ) ? null : clair3_model - def real_clairS_model = (clair3_model == null ) ? null : clairS_model - def real_clairSTO_model = (clair3_model == null ) ? null : clairSTO_model + def real_clairS_model = (clairS_model == null ) ? null : clairS_model + def real_clairSTO_model = (clairSTO_model == null ) ? null : clairSTO_model def paired_data = bam_normal ? true : false def meta_info = meta + [ paired_data: paired_data, platform: method, sex: sex, fiber: fiber, clair3_model: real_clair3_model, clairS_model : real_clairS_model, clairSTO_model: real_clairSTO_model] return [ meta_info, [ bam_tumor ], [ bam_normal ?: [] ] ] @@ -99,6 +99,7 @@ workflow PIPELINE_INITIALISATION { return result } .set { ch_samplesheet } + ch_samplesheet.view() // ch_samplesheet -> meta: [id, paired_data, platform, sex, type] From 6bf8ee8dac17a5ceea62cf16b55e16afd1b3219b Mon Sep 17 00:00:00 2001 From: robert-a-forsyth Date: Mon, 24 Nov 2025 16:34:50 +0100 Subject: [PATCH 20/42] merge + index clairS output --- conf/modules.config | 14 +- modules.json | 25 ++ modules/local/clairs/main.nf | 16 +- .../nf-core/bcftools/concat/environment.yml | 10 + modules/nf-core/bcftools/concat/main.nf | 72 ++++ modules/nf-core/bcftools/concat/meta.yml | 82 ++++ .../bcftools/concat/tests/main.nf.test | 315 ++++++++++++++ .../bcftools/concat/tests/main.nf.test.snap | 395 ++++++++++++++++++ .../bcftools/concat/tests/nextflow.config | 3 + .../bcftools/concat/tests/vcf_gz_index.config | 4 + .../concat/tests/vcf_gz_index_csi.config | 4 + .../concat/tests/vcf_gz_index_tbi.config | 4 + modules/nf-core/bcftools/sort/environment.yml | 10 + modules/nf-core/bcftools/sort/main.nf | 70 ++++ modules/nf-core/bcftools/sort/meta.yml | 71 ++++ .../nf-core/bcftools/sort/tests/main.nf.test | 222 ++++++++++ .../bcftools/sort/tests/main.nf.test.snap | 350 ++++++++++++++++ .../bcftools/sort/tests/vcf_gz_index.config | 4 + .../sort/tests/vcf_gz_index_csi.config | 4 + .../sort/tests/vcf_gz_index_tbi.config | 4 + subworkflows/local/tumor_normal_happhase.nf | 22 +- .../utils_nfcore_lrsomatic_pipeline/main.nf | 1 + tests/default.nf.test.snap | 24 +- 23 files changed, 1705 insertions(+), 21 deletions(-) create mode 100644 modules/nf-core/bcftools/concat/environment.yml create mode 100644 modules/nf-core/bcftools/concat/main.nf create mode 100644 modules/nf-core/bcftools/concat/meta.yml create mode 100644 modules/nf-core/bcftools/concat/tests/main.nf.test create mode 100644 modules/nf-core/bcftools/concat/tests/main.nf.test.snap create mode 100644 modules/nf-core/bcftools/concat/tests/nextflow.config create mode 100644 modules/nf-core/bcftools/concat/tests/vcf_gz_index.config create mode 100644 modules/nf-core/bcftools/concat/tests/vcf_gz_index_csi.config create mode 100644 modules/nf-core/bcftools/concat/tests/vcf_gz_index_tbi.config create mode 100644 modules/nf-core/bcftools/sort/environment.yml create mode 100644 modules/nf-core/bcftools/sort/main.nf create mode 100644 modules/nf-core/bcftools/sort/meta.yml create mode 100644 modules/nf-core/bcftools/sort/tests/main.nf.test create mode 100644 modules/nf-core/bcftools/sort/tests/main.nf.test.snap create mode 100644 modules/nf-core/bcftools/sort/tests/vcf_gz_index.config create mode 100644 modules/nf-core/bcftools/sort/tests/vcf_gz_index_csi.config create mode 100644 modules/nf-core/bcftools/sort/tests/vcf_gz_index_tbi.config diff --git a/conf/modules.config b/conf/modules.config index 95d310d6..9bb7b46f 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -226,7 +226,18 @@ process { // // Small variant calling processes // - + withName: '.*:BCFTOOLS_CONCAT' { + ext.args = '--output-type z' + publishDir = [ + enabled: false + ] + } + withName: '.*:BCFTOOLS_SORT' { + ext.arge = '--output-type z' + publishDir = [ + enabled: false + ] + } withName: '.*:CLAIRSTO' { publishDir = [ path: { "${params.outdir}/${meta.id}/variants/clairsto" }, @@ -236,6 +247,7 @@ process { } withName: '.*:CLAIRS' { + ext.args = '--enable_indel_calling --haplotagged_tumor_bam_provided_so_skip_intermediate_phasing_and_haplotagging' publishDir = [ path: { "${params.outdir}/${meta.id}/variants/clairs" }, mode: params.publish_dir_mode, diff --git a/modules.json b/modules.json index 52190c75..7f7e910d 100644 --- a/modules.json +++ b/modules.json @@ -11,6 +11,21 @@ "installed_by": ["modules"], "patch": "modules/nf-core/ascat/ascat.diff" }, + "bcftools/concat": { + "branch": "master", + "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726", + "installed_by": ["modules", "vcf_gather_bcftools"] + }, + "bcftools/merge": { + "branch": "master", + "git_sha": "f17049e03697726ace7499d2fe342f892594f6f3", + "installed_by": ["modules"] + }, + "bcftools/sort": { + "branch": "master", + "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726", + "installed_by": ["vcf_gather_bcftools"] + }, "ensemblvep/download": { "branch": "master", "git_sha": "2fcc53751152a999bfc9c24f75f494b9e5bb338f", @@ -101,6 +116,11 @@ "installed_by": ["modules"], "patch": "modules/nf-core/severus/severus.diff" }, + "tabix/tabix": { + "branch": "master", + "git_sha": "61846a0d757ff9c0682ba3e28ab0441afd95ad7e", + "installed_by": ["vcf_gather_bcftools"] + }, "untar": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", @@ -139,6 +159,11 @@ "branch": "master", "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e", "installed_by": ["subworkflows"] + }, + "vcf_gather_bcftools": { + "branch": "master", + "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726", + "installed_by": ["subworkflows"] } } } diff --git a/modules/local/clairs/main.nf b/modules/local/clairs/main.nf index e7744781..cef7bbe3 100644 --- a/modules/local/clairs/main.nf +++ b/modules/local/clairs/main.nf @@ -12,9 +12,7 @@ process CLAIRS { tuple val(meta3), path(index) output: - tuple val(meta), path("${prefix}.vcf.gz"), emit: all_vcf - tuple val(meta), path("indel.vcf.gz"), emit: indel_vcf - tuple val(meta), path("snv.vcf.gz"), emit: snv_vcf + tuple val(meta), path("*.vcf.gz"), emit: vcfs tuple val(meta), path("*.vcf.gz.tbi"), emit: tbi path "versions.yml", emit: versions @@ -31,12 +29,14 @@ process CLAIRS { --normal_bam_fn $normal_bam \\ --ref_fn $reference \\ --threads $task.cpus \\ - --enable_indel_calling \\ - --haplotagged_tumor_bam_provided_so_skip_intermediate_phasing_and_haplotagging \\ --platform $model \\ --output_dir . \\ - --output_prefix $prefix \\ + --output_prefix snvs \\ $args + + if [[ -f "snv.vcf.gz" ]]; then + rm snv.vcf.gz + fi cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -49,8 +49,8 @@ process CLAIRS { def prefix = task.ext.prefix ?: "${meta.id}" """ - echo "" | gzip > ${prefix}.vcf.gz - touch ${prefix}.vcf.gz.tbi + echo "" | gzip > snv.vcf.gz + touch snv.vcf.gz.tbi cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/bcftools/concat/environment.yml b/modules/nf-core/bcftools/concat/environment.yml new file mode 100644 index 00000000..ba863b38 --- /dev/null +++ b/modules/nf-core/bcftools/concat/environment.yml @@ -0,0 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + # renovate: datasource=conda depName=bioconda/htslib + - bioconda::htslib=1.22.1 + # renovate: datasource=conda depName=bioconda/bcftools + - bioconda::bcftools=1.22 diff --git a/modules/nf-core/bcftools/concat/main.nf b/modules/nf-core/bcftools/concat/main.nf new file mode 100644 index 00000000..5415b069 --- /dev/null +++ b/modules/nf-core/bcftools/concat/main.nf @@ -0,0 +1,72 @@ +process BCFTOOLS_CONCAT { + tag "$meta.id" + label 'process_medium' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/47/474a5ea8dc03366b04df884d89aeacc4f8e6d1ad92266888e7a8e7958d07cde8/data': + 'community.wave.seqera.io/library/bcftools_htslib:0a3fa2654b52006f' }" + + input: + tuple val(meta), path(vcfs), path(tbi) + + output: + tuple val(meta), path("${prefix}.${extension}") , emit: vcf + tuple val(meta), path("${prefix}.${extension}.tbi"), emit: tbi, optional: true + tuple val(meta), path("${prefix}.${extension}.csi"), emit: csi, optional: true + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + def tbi_names = tbi.findAll { file -> !(file instanceof List) }.collect { file -> file.name } + def create_input_index = vcfs.collect { vcf -> tbi_names.contains(vcf.name + ".tbi") || tbi_names.contains(vcf.name + ".csi") ? "" : "tabix ${vcf}" }.join("\n ") + extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" : + args.contains("--output-type u") || args.contains("-Ou") ? "bcf" : + args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : + args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : + "vcf" + def input = vcfs.sort{it.toString()}.join(" ") + """ + ${create_input_index} + + bcftools concat \\ + --output ${prefix}.${extension} \\ + $args \\ + --threads $task.cpus \\ + ${input} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" : + args.contains("--output-type u") || args.contains("-Ou") ? "bcf" : + args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : + args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : + "vcf" + def index_extension = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" : + args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" : + args.contains("--write-index") || args.contains("-W") ? "csi" : + "" + def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch" + def create_index = extension.endsWith(".gz") && index_extension.matches("csi|tbi") ? "touch ${prefix}.${extension}.${index_extension}" : "" + + """ + ${create_cmd} ${prefix}.${extension} + ${create_index} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') + END_VERSIONS + """ +} diff --git a/modules/nf-core/bcftools/concat/meta.yml b/modules/nf-core/bcftools/concat/meta.yml new file mode 100644 index 00000000..5e14b5a3 --- /dev/null +++ b/modules/nf-core/bcftools/concat/meta.yml @@ -0,0 +1,82 @@ +name: bcftools_concat +description: Concatenate VCF files +keywords: + - variant calling + - concat + - bcftools + - VCF +tools: + - concat: + description: | + Concatenate VCF files. + homepage: http://samtools.github.io/bcftools/bcftools.html + documentation: http://www.htslib.org/doc/bcftools.html + doi: 10.1093/bioinformatics/btp352 + licence: ["MIT"] + identifier: biotools:bcftools +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcfs: + type: list + description: | + List containing 2 or more vcf files + e.g. [ 'file1.vcf', 'file2.vcf' ] + - tbi: + type: list + description: | + List containing 2 or more index files (optional) + e.g. [ 'file1.tbi', 'file2.tbi' ] +output: + vcf: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.${extension}: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" + tbi: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.${extension}.tbi: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.tbi" + csi: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.${extension}.csi: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.csi" + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML +authors: + - "@abhi18av" + - "@nvnieuwk" +maintainers: + - "@abhi18av" + - "@nvnieuwk" diff --git a/modules/nf-core/bcftools/concat/tests/main.nf.test b/modules/nf-core/bcftools/concat/tests/main.nf.test new file mode 100644 index 00000000..442f4b4e --- /dev/null +++ b/modules/nf-core/bcftools/concat/tests/main.nf.test @@ -0,0 +1,315 @@ +nextflow_process { + + name "Test Process BCFTOOLS_CONCAT" + script "../main.nf" + process "BCFTOOLS_CONCAT" + + tag "modules" + tag "modules_nfcore" + tag "bcftools" + tag "bcftools/concat" + + test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]]") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ id:'test3' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz.csi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz.csi', checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index") { + + config "./vcf_gz_index.config" + + when { + process { + """ + input[0] = [ + [ id:'test3' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz.csi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz.csi', checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi") { + + config "./vcf_gz_index_csi.config" + + when { + process { + """ + input[0] = [ + [ id:'test3' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz.csi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz.csi', checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi") { + + config "./vcf_gz_index_tbi.config" + + when { + process { + """ + input[0] = [ + [ id:'test3' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz.csi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz.csi', checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match() }, + { assert process.out.tbi[0][1].endsWith(".tbi") } + ) + } + + } + + + test("homo_sapiens - [[vcf1, vcf2], []]") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ id:'test3' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz', checkIfExists: true) + ], + [] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - stub") { + + config "./nextflow.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test3' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz.csi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz.csi', checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index - stub") { + + config "./vcf_gz_index.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test3' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz.csi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz.csi', checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi - stub") { + + config "./vcf_gz_index_csi.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test3' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz.csi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz.csi', checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi - stub") { + + config "./vcf_gz_index_tbi.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test3' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz.csi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz.csi', checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.tbi[0][1].endsWith(".tbi") } + ) + } + + } + + +} diff --git a/modules/nf-core/bcftools/concat/tests/main.nf.test.snap b/modules/nf-core/bcftools/concat/tests/main.nf.test.snap new file mode 100644 index 00000000..b82169c9 --- /dev/null +++ b/modules/nf-core/bcftools/concat/tests/main.nf.test.snap @@ -0,0 +1,395 @@ +{ + "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi": { + "content": [ + [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz:md5,85db49dd1629d60e1165f491df6348f6" + ] + ], + [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz.csi" + ] + ], + [ + + ], + [ + "versions.yml:md5,689f810ab8f069cb75cfebed99a52df8" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-15T11:26:25.259752" + }, + "homo_sapiens - [[vcf1, vcf2], []]": { + "content": [ + { + "0": [ + [ + { + "id": "test3" + }, + "test3.vcf:md5,bba76244f79c4e307bd0c4c09095885f" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,689f810ab8f069cb75cfebed99a52df8" + ], + "csi": [ + + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "test3" + }, + "test3.vcf:md5,bba76244f79c4e307bd0c4c09095885f" + ] + ], + "versions": [ + "versions.yml:md5,689f810ab8f069cb75cfebed99a52df8" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-15T10:03:17.250013" + }, + "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test3" + }, + "test3.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,689f810ab8f069cb75cfebed99a52df8" + ], + "csi": [ + + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "test3" + }, + "test3.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,689f810ab8f069cb75cfebed99a52df8" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-15T09:52:50.140505" + }, + "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + + ], + "2": [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,689f810ab8f069cb75cfebed99a52df8" + ], + "csi": [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,689f810ab8f069cb75cfebed99a52df8" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-15T09:52:55.544079" + }, + "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi": { + "content": [ + [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz:md5,85db49dd1629d60e1165f491df6348f6" + ] + ], + [ + + ], + [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz.tbi" + ] + ], + [ + "versions.yml:md5,689f810ab8f069cb75cfebed99a52df8" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-15T11:26:31.742638" + }, + "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]]": { + "content": [ + { + "0": [ + [ + { + "id": "test3" + }, + "test3.vcf:md5,bba76244f79c4e307bd0c4c09095885f" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,689f810ab8f069cb75cfebed99a52df8" + ], + "csi": [ + + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "test3" + }, + "test3.vcf:md5,bba76244f79c4e307bd0c4c09095885f" + ] + ], + "versions": [ + "versions.yml:md5,689f810ab8f069cb75cfebed99a52df8" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-15T10:29:33.203302" + }, + "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index": { + "content": [ + [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz:md5,85db49dd1629d60e1165f491df6348f6" + ] + ], + [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz.csi" + ] + ], + [ + + ], + [ + "versions.yml:md5,689f810ab8f069cb75cfebed99a52df8" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-15T11:26:17.482474" + }, + "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,689f810ab8f069cb75cfebed99a52df8" + ], + "csi": [ + + ], + "tbi": [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf": [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,689f810ab8f069cb75cfebed99a52df8" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-15T09:53:07.368971" + }, + "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + + ], + "2": [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,689f810ab8f069cb75cfebed99a52df8" + ], + "csi": [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,689f810ab8f069cb75cfebed99a52df8" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-15T09:53:01.405995" + } +} \ No newline at end of file diff --git a/modules/nf-core/bcftools/concat/tests/nextflow.config b/modules/nf-core/bcftools/concat/tests/nextflow.config new file mode 100644 index 00000000..c6a5142a --- /dev/null +++ b/modules/nf-core/bcftools/concat/tests/nextflow.config @@ -0,0 +1,3 @@ +process { + ext.args = "--no-version" +} diff --git a/modules/nf-core/bcftools/concat/tests/vcf_gz_index.config b/modules/nf-core/bcftools/concat/tests/vcf_gz_index.config new file mode 100644 index 00000000..b6f9165c --- /dev/null +++ b/modules/nf-core/bcftools/concat/tests/vcf_gz_index.config @@ -0,0 +1,4 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z --write-index --no-version --allow-overlaps" +} diff --git a/modules/nf-core/bcftools/concat/tests/vcf_gz_index_csi.config b/modules/nf-core/bcftools/concat/tests/vcf_gz_index_csi.config new file mode 100644 index 00000000..afa03d74 --- /dev/null +++ b/modules/nf-core/bcftools/concat/tests/vcf_gz_index_csi.config @@ -0,0 +1,4 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z --write-index=csi --no-version --allow-overlaps" +} diff --git a/modules/nf-core/bcftools/concat/tests/vcf_gz_index_tbi.config b/modules/nf-core/bcftools/concat/tests/vcf_gz_index_tbi.config new file mode 100644 index 00000000..1ca85231 --- /dev/null +++ b/modules/nf-core/bcftools/concat/tests/vcf_gz_index_tbi.config @@ -0,0 +1,4 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z --write-index=tbi --no-version --allow-overlaps" +} diff --git a/modules/nf-core/bcftools/sort/environment.yml b/modules/nf-core/bcftools/sort/environment.yml new file mode 100644 index 00000000..ba863b38 --- /dev/null +++ b/modules/nf-core/bcftools/sort/environment.yml @@ -0,0 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + # renovate: datasource=conda depName=bioconda/htslib + - bioconda::htslib=1.22.1 + # renovate: datasource=conda depName=bioconda/bcftools + - bioconda::bcftools=1.22 diff --git a/modules/nf-core/bcftools/sort/main.nf b/modules/nf-core/bcftools/sort/main.nf new file mode 100644 index 00000000..80a120b8 --- /dev/null +++ b/modules/nf-core/bcftools/sort/main.nf @@ -0,0 +1,70 @@ +process BCFTOOLS_SORT { + tag "$meta.id" + label 'process_medium' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/47/474a5ea8dc03366b04df884d89aeacc4f8e6d1ad92266888e7a8e7958d07cde8/data': + 'community.wave.seqera.io/library/bcftools_htslib:0a3fa2654b52006f' }" + + input: + tuple val(meta), path(vcf) + + output: + tuple val(meta), path("*_sorted.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf + tuple val(meta), path("*.tbi") , emit: tbi, optional: true + tuple val(meta), path("*.csi") , emit: csi, optional: true + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '--output-type z' + def prefix = task.ext.prefix ?: "${meta.id}" + def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" : + args.contains("--output-type u") || args.contains("-Ou") ? "bcf" : + args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : + args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : + "vcf" + + """ + bcftools \\ + sort \\ + --output ${prefix}_sorted.${extension} \\ + --temp-dir . \\ + $args \\ + $vcf + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '--output-type z' + def prefix = task.ext.prefix ?: "${meta.id}" + + def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" : + args.contains("--output-type u") || args.contains("-Ou") ? "bcf" : + args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : + args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : + "vcf" + def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" : + args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" : + args.contains("--write-index") || args.contains("-W") ? "csi" : + "" + def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch" + def create_index = extension.endsWith(".gz") && index.matches("csi|tbi") ? "touch ${prefix}.${extension}.${index}" : "" + + """ + ${create_cmd} ${prefix}.${extension} + ${create_index} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') + END_VERSIONS + """ +} diff --git a/modules/nf-core/bcftools/sort/meta.yml b/modules/nf-core/bcftools/sort/meta.yml new file mode 100644 index 00000000..c15487c7 --- /dev/null +++ b/modules/nf-core/bcftools/sort/meta.yml @@ -0,0 +1,71 @@ +name: bcftools_sort +description: Sorts VCF files +keywords: + - sorting + - VCF + - variant calling +tools: + - sort: + description: Sort VCF files by coordinates. + homepage: http://samtools.github.io/bcftools/bcftools.html + documentation: http://www.htslib.org/doc/bcftools.html + tool_dev_url: https://github.com/samtools/bcftools + doi: "10.1093/bioinformatics/btp352" + licence: ["MIT"] + identifier: biotools:bcftools +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: The VCF/BCF file to be sorted + pattern: "*.{vcf.gz,vcf,bcf}" + ontologies: [] +output: + vcf: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{vcf,vcf.gz,bcf,bcf.gz}": + type: file + description: Sorted VCF file + pattern: "*.{vcf.gz}" + ontologies: [] + tbi: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: Alternative VCF file index + pattern: "*.tbi" + ontologies: [] + csi: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: Default VCF file index + pattern: "*.csi" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML +authors: + - "@Gwennid" +maintainers: + - "@Gwennid" diff --git a/modules/nf-core/bcftools/sort/tests/main.nf.test b/modules/nf-core/bcftools/sort/tests/main.nf.test new file mode 100644 index 00000000..7d580e4f --- /dev/null +++ b/modules/nf-core/bcftools/sort/tests/main.nf.test @@ -0,0 +1,222 @@ +nextflow_process { + + name "Test Process BCFTOOLS_SORT" + script "../main.nf" + process "BCFTOOLS_SORT" + + tag "modules" + tag "modules_nfcore" + tag "bcftools" + tag "bcftools/sort" + + test("sarscov2 - vcf") { + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match("vcf") } + ) + } + + } + + test("sarscov2 - vcf_gz_index") { + + config "./vcf_gz_index.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - vcf_gz_index_csi") { + + config "./vcf_gz_index_csi.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - vcf_gz_index_tbi") { + + config "./vcf_gz_index_tbi.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match() }, + { assert process.out.tbi[0][1].endsWith(".tbi") } + ) + } + + } + + test("sarscov2 - vcf - stub") { + options "-stub" + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - vcf_gz_index - stub") { + + config "./vcf_gz_index.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - vcf_gz_index_csi - stub") { + + config "./vcf_gz_index_csi.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - vcf_gz_index_tbi - stub") { + + config "./vcf_gz_index_tbi.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.tbi[0][1].endsWith(".tbi") } + ) + } + + } +} diff --git a/modules/nf-core/bcftools/sort/tests/main.nf.test.snap b/modules/nf-core/bcftools/sort/tests/main.nf.test.snap new file mode 100644 index 00000000..3cbca56c --- /dev/null +++ b/modules/nf-core/bcftools/sort/tests/main.nf.test.snap @@ -0,0 +1,350 @@ +{ + "sarscov2 - vcf_gz_index_tbi - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,9699a51675cf58ed9d61b4063de92229" + ], + "csi": [ + + ], + "tbi": [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf": [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,9699a51675cf58ed9d61b4063de92229" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-11T14:49:07.959267" + }, + "vcf": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,8e722884ffb75155212a3fc053918766" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,9699a51675cf58ed9d61b4063de92229" + ], + "csi": [ + + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,8e722884ffb75155212a3fc053918766" + ] + ], + "versions": [ + "versions.yml:md5,9699a51675cf58ed9d61b4063de92229" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-11T14:48:35.236174" + }, + "sarscov2 - vcf_gz_index": { + "content": [ + [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz:md5,8e722884ffb75155212a3fc053918766" + ] + ], + [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz.csi" + ] + ], + [ + + ], + [ + "versions.yml:md5,9699a51675cf58ed9d61b4063de92229" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-11T14:48:39.95133" + }, + "sarscov2 - vcf_gz_index_csi": { + "content": [ + [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz:md5,8e722884ffb75155212a3fc053918766" + ] + ], + [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz.csi" + ] + ], + [ + + ], + [ + "versions.yml:md5,9699a51675cf58ed9d61b4063de92229" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-11T14:48:44.50977" + }, + "sarscov2 - vcf_gz_index - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + + ], + "2": [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,9699a51675cf58ed9d61b4063de92229" + ], + "csi": [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,9699a51675cf58ed9d61b4063de92229" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-11T14:48:58.749279" + }, + "sarscov2 - vcf_gz_index_csi - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + + ], + "2": [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,9699a51675cf58ed9d61b4063de92229" + ], + "csi": [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,9699a51675cf58ed9d61b4063de92229" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-11T14:49:03.283017" + }, + "sarscov2 - vcf - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,9699a51675cf58ed9d61b4063de92229" + ], + "csi": [ + + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,9699a51675cf58ed9d61b4063de92229" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-11T14:48:54.113947" + }, + "sarscov2 - vcf_gz_index_tbi": { + "content": [ + [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz:md5,8e722884ffb75155212a3fc053918766" + ] + ], + [ + + ], + [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz.tbi" + ] + ], + [ + "versions.yml:md5,9699a51675cf58ed9d61b4063de92229" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-11T14:48:48.979311" + } +} \ No newline at end of file diff --git a/modules/nf-core/bcftools/sort/tests/vcf_gz_index.config b/modules/nf-core/bcftools/sort/tests/vcf_gz_index.config new file mode 100644 index 00000000..aacd1346 --- /dev/null +++ b/modules/nf-core/bcftools/sort/tests/vcf_gz_index.config @@ -0,0 +1,4 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z --write-index" +} diff --git a/modules/nf-core/bcftools/sort/tests/vcf_gz_index_csi.config b/modules/nf-core/bcftools/sort/tests/vcf_gz_index_csi.config new file mode 100644 index 00000000..640eb0ba --- /dev/null +++ b/modules/nf-core/bcftools/sort/tests/vcf_gz_index_csi.config @@ -0,0 +1,4 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z --write-index=csi" +} diff --git a/modules/nf-core/bcftools/sort/tests/vcf_gz_index_tbi.config b/modules/nf-core/bcftools/sort/tests/vcf_gz_index_tbi.config new file mode 100644 index 00000000..589a50c6 --- /dev/null +++ b/modules/nf-core/bcftools/sort/tests/vcf_gz_index_tbi.config @@ -0,0 +1,4 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z --write-index=tbi" +} diff --git a/subworkflows/local/tumor_normal_happhase.nf b/subworkflows/local/tumor_normal_happhase.nf index 3d9635ac..c107413c 100644 --- a/subworkflows/local/tumor_normal_happhase.nf +++ b/subworkflows/local/tumor_normal_happhase.nf @@ -3,6 +3,8 @@ include { LONGPHASE_PHASE } from '../../modules/nf-core/longphase/phas include { LONGPHASE_HAPLOTAG } from '../../modules/nf-core/longphase/haplotag/main.nf' include { SAMTOOLS_INDEX } from '../../modules/nf-core/samtools/index/main.nf' include { CLAIRS } from '../../modules/local/clairs/main.nf' +include { BCFTOOLS_CONCAT } from '../../modules/nf-core/bcftools/concat' +include { BCFTOOLS_SORT } from '../../modules/nf-core/bcftools/sort' workflow TUMOR_NORMAL_HAPPHASE { take: @@ -268,10 +270,26 @@ workflow TUMOR_NORMAL_HAPPHASE { fai ) - CLAIRS.out.all_vcf + CLAIRS.out.vcfs + .join(CLAIRS.out.tbi) + .set{clairs_out} + + BCFTOOLS_CONCAT( + clairs_out + ) + + ch_versions = ch_versions.mix(BCFTOOLS_CONCAT.out.versions) + + BCFTOOLS_SORT( + BCFTOOLS_CONCAT.out.vcf + ) + + ch_versions = ch_versions.mix(BCFTOOLS_SORT.out.versions) + + BCFTOOLS_SORT.out.vcf .map { meta, vcf -> def extra = [] - return [meta,vcf, extra] + return [meta, vcf, extra] } .set { somatic_vep } diff --git a/subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf b/subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf index a9266bed..8c3eb330 100644 --- a/subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf @@ -99,6 +99,7 @@ workflow PIPELINE_INITIALISATION { return result } .set { ch_samplesheet } + ch_samplesheet.view() diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 64647d66..3fc27b00 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -1,8 +1,14 @@ { "-profile test": { "content": [ - 78, + 82, { + "BCFTOOLS_CONCAT": { + "bcftools": 1.22 + }, + "BCFTOOLS_SORT": { + "bcftools": 1.22 + }, "CLAIR3": { "clair3": "1.2.0" }, @@ -150,10 +156,9 @@ "sample1/variants/clairs", "sample1/variants/clairs/indel.vcf.gz", "sample1/variants/clairs/indel.vcf.gz.tbi", - "sample1/variants/clairs/sample1.vcf.gz", - "sample1/variants/clairs/sample1.vcf.gz.tbi", - "sample1/variants/clairs/snv.vcf.gz", "sample1/variants/clairs/snv.vcf.gz.tbi", + "sample1/variants/clairs/snvs.vcf.gz", + "sample1/variants/clairs/snvs.vcf.gz.tbi", "sample1/variants/severus", "sample1/variants/severus/all_SVs", "sample1/variants/severus/all_SVs/breakpoint_clusters.tsv", @@ -220,10 +225,9 @@ "sample2/variants/clairs", "sample2/variants/clairs/indel.vcf.gz", "sample2/variants/clairs/indel.vcf.gz.tbi", - "sample2/variants/clairs/sample2.vcf.gz", - "sample2/variants/clairs/sample2.vcf.gz.tbi", - "sample2/variants/clairs/snv.vcf.gz", "sample2/variants/clairs/snv.vcf.gz.tbi", + "sample2/variants/clairs/snvs.vcf.gz", + "sample2/variants/clairs/snvs.vcf.gz.tbi", "sample2/variants/severus", "sample2/variants/severus/all_SVs", "sample2/variants/severus/all_SVs/breakpoint_clusters.tsv", @@ -365,9 +369,9 @@ ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-10-30T17:00:44.230935974" + "timestamp": "2025-11-24T16:33:33.367615182" } } \ No newline at end of file From 2c95ed27eb758feb26c31333dcb7d6659f1aa378 Mon Sep 17 00:00:00 2001 From: robert-a-forsyth Date: Mon, 24 Nov 2025 16:45:31 +0100 Subject: [PATCH 21/42] remove view --- subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf b/subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf index 8c3eb330..787e9f29 100644 --- a/subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf @@ -99,8 +99,7 @@ workflow PIPELINE_INITIALISATION { return result } .set { ch_samplesheet } - - ch_samplesheet.view() + // ch_samplesheet -> meta: [id, paired_data, platform, sex, type] From da63f263051b6d7cde8242dc868b530251597e03 Mon Sep 17 00:00:00 2001 From: robert-a-forsyth Date: Tue, 25 Nov 2025 10:31:11 +0100 Subject: [PATCH 22/42] adjust concat params --- conf/modules.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/modules.config b/conf/modules.config index 9bb7b46f..d82196bb 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -227,7 +227,7 @@ process { // Small variant calling processes // withName: '.*:BCFTOOLS_CONCAT' { - ext.args = '--output-type z' + ext.args = '--output-type z -a' publishDir = [ enabled: false ] From 8af8469eb53b23846a691576fca7e8b5001f4128 Mon Sep 17 00:00:00 2001 From: robert-a-forsyth Date: Tue, 25 Nov 2025 15:05:16 +0100 Subject: [PATCH 23/42] add view --- subworkflows/local/prepare_reference_files.nf | 3 ++- subworkflows/local/tumor_normal_happhase.nf | 6 ++++++ 2 files changed, 8 insertions(+), 1 deletion(-) diff --git a/subworkflows/local/prepare_reference_files.nf b/subworkflows/local/prepare_reference_files.nf index 722b9f73..4b12c54c 100644 --- a/subworkflows/local/prepare_reference_files.nf +++ b/subworkflows/local/prepare_reference_files.nf @@ -39,6 +39,7 @@ workflow PREPARE_REFERENCE_FILES { ch_prepared_fasta = [ [:], fasta ] } + basecall_meta.view() basecall_meta.map { meta, basecall_model_meta, kinetics_meta -> def id_new = basecall_model_meta ?: meta.clair3_model @@ -51,7 +52,7 @@ workflow PREPARE_REFERENCE_FILES { .unique() .set{ model_urls } - + model_urls.view() // // MODULE: Download model // diff --git a/subworkflows/local/tumor_normal_happhase.nf b/subworkflows/local/tumor_normal_happhase.nf index c107413c..09160e9e 100644 --- a/subworkflows/local/tumor_normal_happhase.nf +++ b/subworkflows/local/tumor_normal_happhase.nf @@ -40,6 +40,8 @@ workflow TUMOR_NORMAL_HAPPHASE { } .set{downloaded_model_files} + downloaded_model_files.view() + mixed_bams.normal .map{ meta, bam, bai -> def basecall_model = meta.basecall_model @@ -52,6 +54,8 @@ workflow TUMOR_NORMAL_HAPPHASE { return [ basecall_model, new_meta, bam, bai ] } .set { normal_bams_model } + + normal_bams_model.view() normal_bams_model .combine(downloaded_model_files,by:0) @@ -92,6 +96,8 @@ workflow TUMOR_NORMAL_HAPPHASE { // // small germline variant calling + normal_bam.view() + tumor_bams.view() CLAIR3 ( normal_bams, fasta, From 9851c1f638055d0a84fdfeb300134cf75fdcb8f6 Mon Sep 17 00:00:00 2001 From: robert-a-forsyth Date: Tue, 25 Nov 2025 15:23:57 +0100 Subject: [PATCH 24/42] more view --- workflows/lrsomatic.nf | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/workflows/lrsomatic.nf b/workflows/lrsomatic.nf index 2b84c973..6214cf39 100644 --- a/workflows/lrsomatic.nf +++ b/workflows/lrsomatic.nf @@ -317,7 +317,8 @@ workflow LRSOMATIC { // MODULE: MINIMAP2_ALIGN // // Aligns ubams - + + ch_cat_ubams.view() MINIMAP2_ALIGN ( ch_cat_ubams, ch_fasta, From 160eb79c11584396e1ec671556dddad841f37c09 Mon Sep 17 00:00:00 2001 From: robert-a-forsyth Date: Tue, 25 Nov 2025 15:32:51 +0100 Subject: [PATCH 25/42] view spelling --- subworkflows/local/tumor_normal_happhase.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/tumor_normal_happhase.nf b/subworkflows/local/tumor_normal_happhase.nf index 09160e9e..bca1a1d8 100644 --- a/subworkflows/local/tumor_normal_happhase.nf +++ b/subworkflows/local/tumor_normal_happhase.nf @@ -96,7 +96,7 @@ workflow TUMOR_NORMAL_HAPPHASE { // // small germline variant calling - normal_bam.view() + normal_bams.view() tumor_bams.view() CLAIR3 ( normal_bams, From f746e65233d634ca87c3f9e109f80291fac35e1c Mon Sep 17 00:00:00 2001 From: robert-a-forsyth Date: Wed, 26 Nov 2025 14:22:41 +0100 Subject: [PATCH 26/42] fix channel logic --- modules/local/clairs/main.nf | 1 + subworkflows/local/prepare_reference_files.nf | 2 -- subworkflows/local/tumor_normal_happhase.nf | 3 +-- tests/default.nf.test.snap | 4 +--- 4 files changed, 3 insertions(+), 7 deletions(-) diff --git a/modules/local/clairs/main.nf b/modules/local/clairs/main.nf index cef7bbe3..ce133f43 100644 --- a/modules/local/clairs/main.nf +++ b/modules/local/clairs/main.nf @@ -36,6 +36,7 @@ process CLAIRS { if [[ -f "snv.vcf.gz" ]]; then rm snv.vcf.gz + rm snv.vcf.gz.tbi fi cat <<-END_VERSIONS > versions.yml diff --git a/subworkflows/local/prepare_reference_files.nf b/subworkflows/local/prepare_reference_files.nf index 4b12c54c..5df2b891 100644 --- a/subworkflows/local/prepare_reference_files.nf +++ b/subworkflows/local/prepare_reference_files.nf @@ -39,7 +39,6 @@ workflow PREPARE_REFERENCE_FILES { ch_prepared_fasta = [ [:], fasta ] } - basecall_meta.view() basecall_meta.map { meta, basecall_model_meta, kinetics_meta -> def id_new = basecall_model_meta ?: meta.clair3_model @@ -52,7 +51,6 @@ workflow PREPARE_REFERENCE_FILES { .unique() .set{ model_urls } - model_urls.view() // // MODULE: Download model // diff --git a/subworkflows/local/tumor_normal_happhase.nf b/subworkflows/local/tumor_normal_happhase.nf index bca1a1d8..62e38822 100644 --- a/subworkflows/local/tumor_normal_happhase.nf +++ b/subworkflows/local/tumor_normal_happhase.nf @@ -44,7 +44,7 @@ workflow TUMOR_NORMAL_HAPPHASE { mixed_bams.normal .map{ meta, bam, bai -> - def basecall_model = meta.basecall_model + def basecall_model = (!meta.clair3_model || meta.clair3_model.toString().trim() in ['', '[]']) ? meta.basecall_model : meta.clair3_model def new_meta = [id: meta.id, paired_data: meta.paired_data, platform: meta.platform, @@ -61,7 +61,6 @@ workflow TUMOR_NORMAL_HAPPHASE { .combine(downloaded_model_files,by:0) .map{ basecall_model, meta, bam, bai, meta2, model -> def platform = (meta.platform == "pb") ? "hifi" : "ont" - def clair3_model = (!meta.clair3_model || meta.clair3_model.toString().trim() in ['', '[]']) ? clair3_modelMap.get(meta.basecall_model) : meta.clair3_model return [meta, bam, bai, model, platform] } .set{ normal_bams } diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 3fc27b00..2ee0f8da 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -156,7 +156,6 @@ "sample1/variants/clairs", "sample1/variants/clairs/indel.vcf.gz", "sample1/variants/clairs/indel.vcf.gz.tbi", - "sample1/variants/clairs/snv.vcf.gz.tbi", "sample1/variants/clairs/snvs.vcf.gz", "sample1/variants/clairs/snvs.vcf.gz.tbi", "sample1/variants/severus", @@ -225,7 +224,6 @@ "sample2/variants/clairs", "sample2/variants/clairs/indel.vcf.gz", "sample2/variants/clairs/indel.vcf.gz.tbi", - "sample2/variants/clairs/snv.vcf.gz.tbi", "sample2/variants/clairs/snvs.vcf.gz", "sample2/variants/clairs/snvs.vcf.gz.tbi", "sample2/variants/severus", @@ -372,6 +370,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-24T16:33:33.367615182" + "timestamp": "2025-11-26T14:05:05.064407721" } } \ No newline at end of file From 5b38eee0d7c5ff2bbb00d1a8bc598d523e90917d Mon Sep 17 00:00:00 2001 From: robert-a-forsyth Date: Wed, 26 Nov 2025 15:59:15 +0100 Subject: [PATCH 27/42] lint --- modules.json | 13 +- .../nf-core/bcftools/merge/environment.yml | 10 + modules/nf-core/bcftools/merge/main.nf | 74 ++ modules/nf-core/bcftools/merge/meta.yml | 105 +++ .../nf-core/bcftools/merge/tests/bcf.config | 3 + .../bcftools/merge/tests/bcf_gz.config | 3 + .../nf-core/bcftools/merge/tests/main.nf.test | 853 ++++++++++++++++++ .../bcftools/merge/tests/main.nf.test.snap | 607 +++++++++++++ .../bcftools/merge/tests/nextflow.config | 5 + .../bcftools/merge/tests/nextflow.gvcf.config | 5 + .../nf-core/bcftools/merge/tests/vcf.config | 3 + .../bcftools/merge/tests/vcf_gz.config | 3 + .../bcftools/merge/tests/vcf_gz_index.config | 3 + .../merge/tests/vcf_gz_index_csi.config | 3 + .../merge/tests/vcf_gz_index_tbi.config | 3 + .../nf-core/bcftools/sort/bcftools-sort.diff | 18 + modules/nf-core/bcftools/sort/main.nf | 6 +- 17 files changed, 1703 insertions(+), 14 deletions(-) create mode 100644 modules/nf-core/bcftools/merge/environment.yml create mode 100644 modules/nf-core/bcftools/merge/main.nf create mode 100644 modules/nf-core/bcftools/merge/meta.yml create mode 100644 modules/nf-core/bcftools/merge/tests/bcf.config create mode 100644 modules/nf-core/bcftools/merge/tests/bcf_gz.config create mode 100644 modules/nf-core/bcftools/merge/tests/main.nf.test create mode 100644 modules/nf-core/bcftools/merge/tests/main.nf.test.snap create mode 100644 modules/nf-core/bcftools/merge/tests/nextflow.config create mode 100644 modules/nf-core/bcftools/merge/tests/nextflow.gvcf.config create mode 100644 modules/nf-core/bcftools/merge/tests/vcf.config create mode 100644 modules/nf-core/bcftools/merge/tests/vcf_gz.config create mode 100644 modules/nf-core/bcftools/merge/tests/vcf_gz_index.config create mode 100644 modules/nf-core/bcftools/merge/tests/vcf_gz_index_csi.config create mode 100644 modules/nf-core/bcftools/merge/tests/vcf_gz_index_tbi.config create mode 100644 modules/nf-core/bcftools/sort/bcftools-sort.diff diff --git a/modules.json b/modules.json index 7f7e910d..58f3aae4 100644 --- a/modules.json +++ b/modules.json @@ -24,7 +24,8 @@ "bcftools/sort": { "branch": "master", "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726", - "installed_by": ["vcf_gather_bcftools"] + "installed_by": ["vcf_gather_bcftools"], + "patch": "modules/nf-core/bcftools/sort/bcftools-sort.diff" }, "ensemblvep/download": { "branch": "master", @@ -116,11 +117,6 @@ "installed_by": ["modules"], "patch": "modules/nf-core/severus/severus.diff" }, - "tabix/tabix": { - "branch": "master", - "git_sha": "61846a0d757ff9c0682ba3e28ab0441afd95ad7e", - "installed_by": ["vcf_gather_bcftools"] - }, "untar": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", @@ -159,11 +155,6 @@ "branch": "master", "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e", "installed_by": ["subworkflows"] - }, - "vcf_gather_bcftools": { - "branch": "master", - "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726", - "installed_by": ["subworkflows"] } } } diff --git a/modules/nf-core/bcftools/merge/environment.yml b/modules/nf-core/bcftools/merge/environment.yml new file mode 100644 index 00000000..ba863b38 --- /dev/null +++ b/modules/nf-core/bcftools/merge/environment.yml @@ -0,0 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + # renovate: datasource=conda depName=bioconda/htslib + - bioconda::htslib=1.22.1 + # renovate: datasource=conda depName=bioconda/bcftools + - bioconda::bcftools=1.22 diff --git a/modules/nf-core/bcftools/merge/main.nf b/modules/nf-core/bcftools/merge/main.nf new file mode 100644 index 00000000..c560a902 --- /dev/null +++ b/modules/nf-core/bcftools/merge/main.nf @@ -0,0 +1,74 @@ +process BCFTOOLS_MERGE { + tag "$meta.id" + label 'process_medium' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/47/474a5ea8dc03366b04df884d89aeacc4f8e6d1ad92266888e7a8e7958d07cde8/data': + 'community.wave.seqera.io/library/bcftools_htslib:0a3fa2654b52006f' }" + + input: + tuple val(meta), path(vcfs), path(tbis) + tuple val(meta2), path(fasta) + tuple val(meta3), path(fai) + tuple val(meta4), path(bed) + + output: + tuple val(meta), path("*.{bcf,vcf}{,.gz}"), emit: vcf + tuple val(meta), path("*.{csi,tbi}") , emit: index, optional: true + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + + def input = (vcfs.collect().size() > 1) ? vcfs.sort{ it.name } : vcfs + def regions = bed ? "--regions-file $bed" : "" + def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" : + args.contains("--output-type u") || args.contains("-Ou") ? "bcf" : + args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : + args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : + "vcf" + + """ + bcftools merge \\ + $args \\ + $regions \\ + --threads $task.cpus \\ + --output ${prefix}.${extension} \\ + $input + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" : + args.contains("--output-type u") || args.contains("-Ou") ? "bcf" : + args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : + args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : + "vcf" + def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" : + args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" : + args.contains("--write-index") || args.contains("-W") ? "csi" : + "" + def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch" + def create_index = extension.endsWith(".gz") && index.matches("csi|tbi") ? "touch ${prefix}.${extension}.${index}" : "" + + """ + ${create_cmd} ${prefix}.${extension} + ${create_index} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') + END_VERSIONS + """ +} diff --git a/modules/nf-core/bcftools/merge/meta.yml b/modules/nf-core/bcftools/merge/meta.yml new file mode 100644 index 00000000..09af245a --- /dev/null +++ b/modules/nf-core/bcftools/merge/meta.yml @@ -0,0 +1,105 @@ +name: bcftools_merge +description: Merge VCF files +keywords: + - variant calling + - merge + - VCF +tools: + - merge: + description: | + Merge VCF files. + homepage: http://samtools.github.io/bcftools/bcftools.html + documentation: http://www.htslib.org/doc/bcftools.html + doi: 10.1093/bioinformatics/btp352 + licence: ["MIT"] + identifier: biotools:bcftools +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcfs: + type: file + description: | + List containing 2 or more vcf files + e.g. [ 'file1.vcf', 'file2.vcf' ] + ontologies: [] + - tbis: + type: file + description: | + List containing the tbi index files corresponding to the vcfs input files + e.g. [ 'file1.vcf.tbi', 'file2.vcf.tbi' ] + ontologies: [] + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: "(Optional) The fasta reference file (only necessary for the `--gvcf + FILE` parameter)" + pattern: "*.{fasta,fa}" + ontologies: [] + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: "(Optional) The fasta reference file index (only necessary for + the `--gvcf FILE` parameter)" + pattern: "*.fai" + ontologies: [] + - - meta4: + type: map + description: | + Groovy Map containing bed information + e.g. [ id:'genome' ] + - bed: + type: file + description: "(Optional) The bed regions to merge on" + pattern: "*.bed" + ontologies: [] +output: + vcf: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{bcf,vcf}{,.gz}": + type: file + description: merged output file + pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" + ontologies: [] + index: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{csi,tbi}": + type: file + description: index of merged output + pattern: "*.{csi,tbi}" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML +authors: + - "@joseespinosa" + - "@drpatelh" + - "@nvnieuwk" + - "@ramprasadn" +maintainers: + - "@joseespinosa" + - "@drpatelh" + - "@nvnieuwk" + - "@ramprasadn" diff --git a/modules/nf-core/bcftools/merge/tests/bcf.config b/modules/nf-core/bcftools/merge/tests/bcf.config new file mode 100644 index 00000000..4467d07d --- /dev/null +++ b/modules/nf-core/bcftools/merge/tests/bcf.config @@ -0,0 +1,3 @@ +process { + ext.args = '--output-type u --no-version' +} diff --git a/modules/nf-core/bcftools/merge/tests/bcf_gz.config b/modules/nf-core/bcftools/merge/tests/bcf_gz.config new file mode 100644 index 00000000..280de8db --- /dev/null +++ b/modules/nf-core/bcftools/merge/tests/bcf_gz.config @@ -0,0 +1,3 @@ +process { + ext.args = '--output-type b --no-version' +} diff --git a/modules/nf-core/bcftools/merge/tests/main.nf.test b/modules/nf-core/bcftools/merge/tests/main.nf.test new file mode 100644 index 00000000..3995fc1a --- /dev/null +++ b/modules/nf-core/bcftools/merge/tests/main.nf.test @@ -0,0 +1,853 @@ +nextflow_process { + + name "Test Process BCFTOOLS_MERGE" + script "../main.nf" + process "BCFTOOLS_MERGE" + + tag "modules" + tag "modules_nfcore" + tag "bcftools" + tag "bcftools/merge" + + test("sarscov2 - [vcf, tbi], [], [], []") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf") }, + { assert snapshot( + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, + process.out.versions, + ).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - vcf output") { + + config "./vcf.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf") }, + { assert snapshot( + path(process.out.vcf.get(0).get(1)).md5, + process.out.versions, + ).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output") { + + config "./vcf_gz.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf.gz") }, + { assert snapshot( + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, + process.out.versions, + ).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - bcf output") { + + config "./bcf.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("bcf") }, + { assert snapshot( + file(process.out.vcf.get(0).get(1)).name, + process.out.versions, + ).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - bcf.gz output") { + + config "./bcf_gz.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("bcf.gz") }, + { assert snapshot( + file(process.out.vcf.get(0).get(1)).name, + process.out.versions, + ).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - index") { + + config "./vcf_gz_index.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf.gz") }, + { assert process.out.index.get(0).get(1).endsWith("csi") }, + { assert snapshot( + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, + file(process.out.index.get(0).get(1)).name, + process.out.versions, + ).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - csi index") { + + config "./vcf_gz_index_csi.config" + + when { + + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf.gz") }, + { assert process.out.index.get(0).get(1).endsWith("csi") }, + { assert snapshot( + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, + file(process.out.index.get(0).get(1)).name, + process.out.versions, + ).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - tbi index") { + + config "./vcf_gz_index_tbi.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf.gz") }, + { assert process.out.index.get(0).get(1).endsWith("tbi") }, + { assert snapshot( + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, + file(process.out.index.get(0).get(1)).name, + process.out.versions, + ).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], bed") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [ + [ id:'test' ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf") }, + { assert snapshot( + path(process.out.vcf.get(0).get(1)).md5, + process.out.versions, + ).match() } + ) + } + + } + + test("homo_sapiens - [vcf, tbi], fasta, fai, bed - vcf.gz output") { + + config "./nextflow.gvcf.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [ + [ id:'test' ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + ] + input[2] = [ + [ id:'test' ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] + ] + input[3] = [ + [ id:'test' ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf.gz") }, + { assert snapshot( + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, + process.out.versions, + ).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - one sample") { + + config "./nextflow.config" + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf") }, + { assert snapshot( + path(process.out.vcf.get(0).get(1)).md5, + process.out.versions, + ).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - stub") { + + options "-stub" + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf") }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - vcf output - stub") { + + options "-stub" + config "./vcf.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf") }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - stub") { + + options "-stub" + config "./vcf_gz.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf.gz") }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - bcf output - stub") { + + options "-stub" + config "./bcf.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("bcf") }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - bcf.gz output - stub") { + + options "-stub" + config "./bcf_gz.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("bcf.gz") }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - index - stub") { + + options "-stub" + config "./vcf_gz_index.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf.gz") }, + { assert process.out.index.get(0).get(1).endsWith("csi") }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - csi index - stub") { + + options "-stub" + config "./vcf_gz_index_csi.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf.gz") }, + { assert process.out.index.get(0).get(1).endsWith("csi") }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - tbi index - stub") { + + options "-stub" + config "./vcf_gz_index_tbi.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf.gz") }, + { assert process.out.index.get(0).get(1).endsWith("tbi") }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], bed - stub") { + + options "-stub" + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [ + [ id:'test' ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf") }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("homo_sapiens - [vcf, tbi], fasta, fai, bed - vcf.gz output - stub") { + + options "-stub" + config "./nextflow.gvcf.config" + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz.tbi', checkIfExists: true), + ] + ] + input[1] = [ + [ id:'test' ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + ] + input[2] = [ + [ id:'test' ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] + ] + input[3] = [ + [ id:'test' ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf.gz") }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - one sample - stub") { + + options "-stub" + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf") }, + { assert snapshot(process.out).match() } + ) + } + + } +} diff --git a/modules/nf-core/bcftools/merge/tests/main.nf.test.snap b/modules/nf-core/bcftools/merge/tests/main.nf.test.snap new file mode 100644 index 00000000..d340b7b4 --- /dev/null +++ b/modules/nf-core/bcftools/merge/tests/main.nf.test.snap @@ -0,0 +1,607 @@ +{ + "sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - tbi index": { + "content": [ + "e0de448dc8e712956a03ce68d79a0b3a", + "test.vcf.gz.tbi", + [ + "versions.yml:md5,46d60729adb9ea9a4e4ab722b487a56b" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-11T14:20:16.859885" + }, + "sarscov2 - [vcf, tbi], [], [], [] - vcf output - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + 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output": { + "content": [ + "e0de448dc8e712956a03ce68d79a0b3a", + [ + "versions.yml:md5,46d60729adb9ea9a4e4ab722b487a56b" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-11T14:19:51.935426" + }, + "sarscov2 - [vcf, tbi], [], [], bed - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,46d60729adb9ea9a4e4ab722b487a56b" + ], + "index": [ + + ], + "vcf": [ + [ + { + "id": "test" + }, + "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,46d60729adb9ea9a4e4ab722b487a56b" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-11T14:21:18.319666" + }, + "sarscov2 - [vcf, tbi], [], [], [] - bcf output": { + "content": [ + "test.bcf", + [ + "versions.yml:md5,46d60729adb9ea9a4e4ab722b487a56b" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-11T14:19:56.742352" + }, + "sarscov2 - [vcf, tbi], [], [], [] - bcf output - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.bcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,46d60729adb9ea9a4e4ab722b487a56b" + ], + "index": [ + + ], + "vcf": [ + [ + { + "id": "test" + }, + "test.bcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,46d60729adb9ea9a4e4ab722b487a56b" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-11T14:20:53.962449" + }, + "sarscov2 - [vcf, tbi], [], [], [] - one sample - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,46d60729adb9ea9a4e4ab722b487a56b" + ], + "index": [ + + ], + "vcf": [ + [ + { + "id": "test" + }, + "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,46d60729adb9ea9a4e4ab722b487a56b" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-11T14:21:29.155018" + }, + "homo_sapiens - [vcf, tbi], fasta, fai, bed - vcf.gz output - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,46d60729adb9ea9a4e4ab722b487a56b" + ], + "index": [ + + ], + "vcf": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,46d60729adb9ea9a4e4ab722b487a56b" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-11T14:21:23.944931" + }, + "sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - index": { + "content": [ + "e0de448dc8e712956a03ce68d79a0b3a", + "test.vcf.gz.csi", + [ + "versions.yml:md5,46d60729adb9ea9a4e4ab722b487a56b" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-11T14:20:06.894016" + }, + "homo_sapiens - [vcf, tbi], fasta, fai, bed - vcf.gz output": { + "content": [ + "645b7f7f9131bfe350a9ec3cf82c17fe", + [ + "versions.yml:md5,46d60729adb9ea9a4e4ab722b487a56b" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-11T14:20:28.149857" + }, + "sarscov2 - [vcf, tbi], [], [], [] - one sample": { + "content": [ + "2a374cf02f0c32cf607646167e7f153b", + [ + "versions.yml:md5,46d60729adb9ea9a4e4ab722b487a56b" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-11T14:20:32.592911" + }, + "sarscov2 - [vcf, tbi], [], [], [] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,46d60729adb9ea9a4e4ab722b487a56b" + ], + "index": [ + + ], + "vcf": [ + [ + { + "id": "test" + }, + "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,46d60729adb9ea9a4e4ab722b487a56b" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-11T14:20:37.830691" + }, + "sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - csi index - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,46d60729adb9ea9a4e4ab722b487a56b" + ], + "index": [ + [ + { + "id": "test" + }, + "test.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,46d60729adb9ea9a4e4ab722b487a56b" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-11T14:21:08.5748" + }, + "sarscov2 - [vcf, tbi], [], [], []": { + "content": [ + "e0de448dc8e712956a03ce68d79a0b3a", + [ + "versions.yml:md5,46d60729adb9ea9a4e4ab722b487a56b" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-11T14:19:41.986954" + }, + "sarscov2 - [vcf, tbi], [], [], [] - bcf.gz output": { + "content": [ + "test.bcf.gz", + [ + "versions.yml:md5,46d60729adb9ea9a4e4ab722b487a56b" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-11T14:20:01.801297" + } +} \ No newline at end of file diff --git a/modules/nf-core/bcftools/merge/tests/nextflow.config b/modules/nf-core/bcftools/merge/tests/nextflow.config new file mode 100644 index 00000000..c3f0b715 --- /dev/null +++ b/modules/nf-core/bcftools/merge/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: BCFTOOLS_MERGE { + ext.args = '--force-samples --force-single --no-version' + } +} diff --git a/modules/nf-core/bcftools/merge/tests/nextflow.gvcf.config b/modules/nf-core/bcftools/merge/tests/nextflow.gvcf.config new file mode 100644 index 00000000..8c457b71 --- /dev/null +++ b/modules/nf-core/bcftools/merge/tests/nextflow.gvcf.config @@ -0,0 +1,5 @@ +process { + withName: BCFTOOLS_MERGE { + ext.args = { "--force-samples --no-version --output-type z --gvcf $fasta" } + } +} diff --git a/modules/nf-core/bcftools/merge/tests/vcf.config b/modules/nf-core/bcftools/merge/tests/vcf.config new file mode 100644 index 00000000..759222e5 --- /dev/null +++ b/modules/nf-core/bcftools/merge/tests/vcf.config @@ -0,0 +1,3 @@ +process { + ext.args = '--output-type v --no-version' +} diff --git a/modules/nf-core/bcftools/merge/tests/vcf_gz.config b/modules/nf-core/bcftools/merge/tests/vcf_gz.config new file mode 100644 index 00000000..8b6ad8b4 --- /dev/null +++ b/modules/nf-core/bcftools/merge/tests/vcf_gz.config @@ -0,0 +1,3 @@ +process { + ext.args = '--output-type z --no-version' +} diff --git a/modules/nf-core/bcftools/merge/tests/vcf_gz_index.config b/modules/nf-core/bcftools/merge/tests/vcf_gz_index.config new file mode 100644 index 00000000..9f1e9b1d --- /dev/null +++ b/modules/nf-core/bcftools/merge/tests/vcf_gz_index.config @@ -0,0 +1,3 @@ +process { + ext.args = "--output-type z --write-index --no-version" +} diff --git a/modules/nf-core/bcftools/merge/tests/vcf_gz_index_csi.config b/modules/nf-core/bcftools/merge/tests/vcf_gz_index_csi.config new file mode 100644 index 00000000..8308ee1a --- /dev/null +++ b/modules/nf-core/bcftools/merge/tests/vcf_gz_index_csi.config @@ -0,0 +1,3 @@ +process { + ext.args = "--output-type z --write-index=csi --no-version" +} diff --git a/modules/nf-core/bcftools/merge/tests/vcf_gz_index_tbi.config b/modules/nf-core/bcftools/merge/tests/vcf_gz_index_tbi.config new file mode 100644 index 00000000..9be4075b --- /dev/null +++ b/modules/nf-core/bcftools/merge/tests/vcf_gz_index_tbi.config @@ -0,0 +1,3 @@ +process { + ext.args = "--output-type z --write-index=tbi --no-version" +} diff --git a/modules/nf-core/bcftools/sort/bcftools-sort.diff b/modules/nf-core/bcftools/sort/bcftools-sort.diff new file mode 100644 index 00000000..b1696f25 --- /dev/null +++ b/modules/nf-core/bcftools/sort/bcftools-sort.diff @@ -0,0 +1,18 @@ +Changes in component 'nf-core/bcftools/sort' +'modules/nf-core/bcftools/sort/meta.yml' is unchanged +Changes in 'bcftools/sort/main.nf': +--- modules/nf-core/bcftools/sort/main.nf ++++ modules/nf-core/bcftools/sort/main.nf +@@ -67,4 +67,4 @@ + bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') + END_VERSIONS + """ +-} ++} +'modules/nf-core/bcftools/sort/environment.yml' is unchanged +'modules/nf-core/bcftools/sort/tests/vcf_gz_index.config' is unchanged +'modules/nf-core/bcftools/sort/tests/main.nf.test' is unchanged +'modules/nf-core/bcftools/sort/tests/vcf_gz_index_csi.config' is unchanged +'modules/nf-core/bcftools/sort/tests/vcf_gz_index_tbi.config' is unchanged +'modules/nf-core/bcftools/sort/tests/main.nf.test.snap' is unchanged +************************************************************ diff --git a/modules/nf-core/bcftools/sort/main.nf b/modules/nf-core/bcftools/sort/main.nf index 80a120b8..5040f0cb 100644 --- a/modules/nf-core/bcftools/sort/main.nf +++ b/modules/nf-core/bcftools/sort/main.nf @@ -11,7 +11,7 @@ process BCFTOOLS_SORT { tuple val(meta), path(vcf) output: - tuple val(meta), path("*_sorted.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf + tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf tuple val(meta), path("*.tbi") , emit: tbi, optional: true tuple val(meta), path("*.csi") , emit: csi, optional: true path "versions.yml" , emit: versions @@ -31,7 +31,7 @@ process BCFTOOLS_SORT { """ bcftools \\ sort \\ - --output ${prefix}_sorted.${extension} \\ + --output ${prefix}.${extension} \\ --temp-dir . \\ $args \\ $vcf @@ -67,4 +67,4 @@ process BCFTOOLS_SORT { bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') END_VERSIONS """ -} +} \ No newline at end of file From dac7854c5f7dc32a9afa5b6394a486347249e568 Mon Sep 17 00:00:00 2001 From: robert-a-forsyth Date: Wed, 26 Nov 2025 16:08:56 +0100 Subject: [PATCH 28/42] lint --- .github/workflows/linting.yml | 16 ++++++++-------- .github/workflows/linting_comment.yml | 2 +- .prettierignore | 3 +++ 3 files changed, 12 insertions(+), 9 deletions(-) diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 8b0f88c3..7a527a34 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -11,12 +11,12 @@ jobs: pre-commit: runs-on: ubuntu-latest steps: - - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 - - name: Set up Python 3.13 - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5 + - name: Set up Python 3.14 + uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6 with: - python-version: "3.13" + python-version: "3.14" - name: Install pre-commit run: pip install pre-commit @@ -28,14 +28,14 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 - name: Install Nextflow uses: nf-core/setup-nextflow@v2 - - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5 + - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6 with: - python-version: "3.13" + python-version: "3.14" architecture: "x64" - name: read .nf-core.yml @@ -71,7 +71,7 @@ jobs: - name: Upload linting log file artifact if: ${{ always() }} - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4 + uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5 with: name: linting-logs path: | diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index d43797d9..e6e9bc26 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -21,7 +21,7 @@ jobs: run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT - name: Post PR comment - uses: marocchino/sticky-pull-request-comment@52423e01640425a022ef5fd42c6fb5f633a02728 # v2 + uses: marocchino/sticky-pull-request-comment@773744901bac0e8cbb5a0dc842800d45e9b2b405 # v2 with: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} number: ${{ steps.pr_number.outputs.pr_number }} diff --git a/.prettierignore b/.prettierignore index edd29f01..dd749d43 100644 --- a/.prettierignore +++ b/.prettierignore @@ -10,4 +10,7 @@ testing/ testing* *.pyc bin/ +.nf-test/ ro-crate-metadata.json +modules/nf-core/ +subworkflows/nf-core/ From 87bc1489608e398936bfee5a57602f297ddc55e4 Mon Sep 17 00:00:00 2001 From: robert-a-forsyth Date: Wed, 26 Nov 2025 16:11:46 +0100 Subject: [PATCH 29/42] prettier --- modules/local/clairs/main.nf | 2 +- subworkflows/local/tumor_normal_happhase.nf | 4 ++-- workflows/lrsomatic.nf | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/modules/local/clairs/main.nf b/modules/local/clairs/main.nf index ce133f43..d4368bf6 100644 --- a/modules/local/clairs/main.nf +++ b/modules/local/clairs/main.nf @@ -33,7 +33,7 @@ process CLAIRS { --output_dir . \\ --output_prefix snvs \\ $args - + if [[ -f "snv.vcf.gz" ]]; then rm snv.vcf.gz rm snv.vcf.gz.tbi diff --git a/subworkflows/local/tumor_normal_happhase.nf b/subworkflows/local/tumor_normal_happhase.nf index 62e38822..478188d4 100644 --- a/subworkflows/local/tumor_normal_happhase.nf +++ b/subworkflows/local/tumor_normal_happhase.nf @@ -54,7 +54,7 @@ workflow TUMOR_NORMAL_HAPPHASE { return [ basecall_model, new_meta, bam, bai ] } .set { normal_bams_model } - + normal_bams_model.view() normal_bams_model @@ -278,7 +278,7 @@ workflow TUMOR_NORMAL_HAPPHASE { CLAIRS.out.vcfs .join(CLAIRS.out.tbi) .set{clairs_out} - + BCFTOOLS_CONCAT( clairs_out ) diff --git a/workflows/lrsomatic.nf b/workflows/lrsomatic.nf index 6214cf39..d76e3bfb 100644 --- a/workflows/lrsomatic.nf +++ b/workflows/lrsomatic.nf @@ -317,7 +317,7 @@ workflow LRSOMATIC { // MODULE: MINIMAP2_ALIGN // // Aligns ubams - + ch_cat_ubams.view() MINIMAP2_ALIGN ( ch_cat_ubams, From 7cd789825fdec494bece985aae4684def31c1faf Mon Sep 17 00:00:00 2001 From: robert-a-forsyth Date: Thu, 27 Nov 2025 10:38:53 +0100 Subject: [PATCH 30/42] fix channel meta --- modules.json | 115 +++++++++++++++----- modules/nf-core/bcftools/sort/main.nf | 2 +- subworkflows/local/tumor_normal_happhase.nf | 18 ++- tests/default.nf.test.snap | 2 +- workflows/lrsomatic.nf | 1 - 5 files changed, 96 insertions(+), 42 deletions(-) diff --git a/modules.json b/modules.json index 58f3aae4..4afad53b 100644 --- a/modules.json +++ b/modules.json @@ -8,129 +8,178 @@ "ascat": { "branch": "master", "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", - "installed_by": ["modules"], + "installed_by": [ + "modules" + ], "patch": "modules/nf-core/ascat/ascat.diff" }, "bcftools/concat": { "branch": "master", "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726", - "installed_by": ["modules", "vcf_gather_bcftools"] + "installed_by": [ + "modules", + "vcf_gather_bcftools" + ] }, "bcftools/merge": { "branch": "master", "git_sha": "f17049e03697726ace7499d2fe342f892594f6f3", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/sort": { "branch": "master", "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726", - "installed_by": ["vcf_gather_bcftools"], + "installed_by": [ + "vcf_gather_bcftools" + ], "patch": "modules/nf-core/bcftools/sort/bcftools-sort.diff" }, "ensemblvep/download": { "branch": "master", "git_sha": "2fcc53751152a999bfc9c24f75f494b9e5bb338f", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "ensemblvep/vep": { "branch": "master", "git_sha": "48ca3de1737b0144aa9fe05bea2b681f0ae45a95", - "installed_by": ["modules"], + "installed_by": [ + "modules" + ], "patch": "modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff" }, "longphase/haplotag": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "longphase/phase": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"], + "installed_by": [ + "modules" + ], "patch": "modules/nf-core/longphase/phase/longphase-phase.diff" }, "minimap2/align": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"], + "installed_by": [ + "modules" + ], "patch": "modules/nf-core/minimap2/align/minimap2-align.diff" }, "minimap2/index": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "modkit/pileup": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "mosdepth": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "multiqc": { "branch": "master", "git_sha": "a4488d3d09244f29fb4606ba4eef85d59dcc6ad8", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "pigz/uncompress": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/cat": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/faidx": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/flagstat": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["bam_stats_samtools"] + "installed_by": [ + "bam_stats_samtools" + ] }, "samtools/idxstats": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["bam_stats_samtools"] + "installed_by": [ + "bam_stats_samtools" + ] }, "samtools/index": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/stats": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["bam_stats_samtools"], + "installed_by": [ + "bam_stats_samtools" + ], "patch": "modules/nf-core/samtools/stats/samtools-stats.diff" }, "severus": { "branch": "master", "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", - "installed_by": ["modules"], + "installed_by": [ + "modules" + ], "patch": "modules/nf-core/severus/severus.diff" }, "untar": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "unzip": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "wget": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] } } }, @@ -139,25 +188,33 @@ "bam_stats_samtools": { "branch": "master", "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nextflow_pipeline": { "branch": "master", "git_sha": "c2b22d85f30a706a3073387f30380704fcae013b", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "51ae5406a030d4da1e49e4dab49756844fdd6c7a", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nfschema_plugin": { "branch": "master", "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] } } } } } -} +} \ No newline at end of file diff --git a/modules/nf-core/bcftools/sort/main.nf b/modules/nf-core/bcftools/sort/main.nf index 5040f0cb..302c7311 100644 --- a/modules/nf-core/bcftools/sort/main.nf +++ b/modules/nf-core/bcftools/sort/main.nf @@ -31,7 +31,7 @@ process BCFTOOLS_SORT { """ bcftools \\ sort \\ - --output ${prefix}.${extension} \\ + --output ${prefix}.sorted.${extension} \\ --temp-dir . \\ $args \\ $vcf diff --git a/subworkflows/local/tumor_normal_happhase.nf b/subworkflows/local/tumor_normal_happhase.nf index 478188d4..5be12daa 100644 --- a/subworkflows/local/tumor_normal_happhase.nf +++ b/subworkflows/local/tumor_normal_happhase.nf @@ -40,7 +40,6 @@ workflow TUMOR_NORMAL_HAPPHASE { } .set{downloaded_model_files} - downloaded_model_files.view() mixed_bams.normal .map{ meta, bam, bai -> @@ -50,12 +49,12 @@ workflow TUMOR_NORMAL_HAPPHASE { platform: meta.platform, sex: meta.sex, fiber: meta.fiber, - basecall_model: meta.basecall_model] + basecall_model: meta.basecall_model, + clairS_model: meta.clairS_model] return [ basecall_model, new_meta, bam, bai ] } .set { normal_bams_model } - - normal_bams_model.view() + normal_bams_model .combine(downloaded_model_files,by:0) @@ -81,7 +80,8 @@ workflow TUMOR_NORMAL_HAPPHASE { platform: meta.platform, sex: meta.sex, fiber: meta.fiber, - basecall_model: meta.basecall_model] + basecall_model: meta.basecall_model, + clairS_model: meta.clairS_model] return[new_meta, bam, bai] } .set{ tumor_bams } @@ -94,9 +94,6 @@ workflow TUMOR_NORMAL_HAPPHASE { // MODULE: CLAIR3 // // small germline variant calling - - normal_bams.view() - tumor_bams.view() CLAIR3 ( normal_bams, fasta, @@ -234,7 +231,8 @@ workflow TUMOR_NORMAL_HAPPHASE { platform: meta.platform, sex: meta.sex, fiber: meta.fiber, - basecall_model: meta.basecall_model] + basecall_model: meta.basecall_model, + clairS_model: meta.clairS_model] return[new_meta, [[type: meta.type], hapbam], [[type: meta.type], hapbai]] } .groupTuple(size: 2) @@ -278,7 +276,7 @@ workflow TUMOR_NORMAL_HAPPHASE { CLAIRS.out.vcfs .join(CLAIRS.out.tbi) .set{clairs_out} - + BCFTOOLS_CONCAT( clairs_out ) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 2ee0f8da..52651ce4 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -370,6 +370,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-26T14:05:05.064407721" + "timestamp": "2025-11-27T10:35:33.023032177" } } \ No newline at end of file diff --git a/workflows/lrsomatic.nf b/workflows/lrsomatic.nf index d76e3bfb..2b84c973 100644 --- a/workflows/lrsomatic.nf +++ b/workflows/lrsomatic.nf @@ -318,7 +318,6 @@ workflow LRSOMATIC { // // Aligns ubams - ch_cat_ubams.view() MINIMAP2_ALIGN ( ch_cat_ubams, ch_fasta, From 9e86276782b7bb6577e5ef3a96817d9cc403901f Mon Sep 17 00:00:00 2001 From: robert-a-forsyth Date: Thu, 27 Nov 2025 13:36:58 +0100 Subject: [PATCH 31/42] view --- subworkflows/local/tumor_normal_happhase.nf | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/subworkflows/local/tumor_normal_happhase.nf b/subworkflows/local/tumor_normal_happhase.nf index 5be12daa..f5326742 100644 --- a/subworkflows/local/tumor_normal_happhase.nf +++ b/subworkflows/local/tumor_normal_happhase.nf @@ -30,6 +30,8 @@ workflow TUMOR_NORMAL_HAPPHASE { } .set{ mixed_bams } + mixed_bams.view() + // Get normal bams and add platform/model info for Clair3 usage // remove type from so that information can be merged easier later @@ -55,6 +57,7 @@ workflow TUMOR_NORMAL_HAPPHASE { } .set { normal_bams_model } + normal_bams_model.view() normal_bams_model .combine(downloaded_model_files,by:0) @@ -64,6 +67,7 @@ workflow TUMOR_NORMAL_HAPPHASE { } .set{ normal_bams } + normal_bams.view() // normal_bams -> meta: [id, paired_data, platform, sex, fiber, basecall_model] // bam: list of concatenated aligned bams // bai: indexes for bam files @@ -86,6 +90,7 @@ workflow TUMOR_NORMAL_HAPPHASE { } .set{ tumor_bams } + tumor_bams.view() // tumor_bams -> meta: [id, paired_data, platform, sex, fiber, basecall_model] // bam: list of concatenated aligned bams // bai: indexes for bam files @@ -113,6 +118,8 @@ workflow TUMOR_NORMAL_HAPPHASE { return [meta, bam, bai, vcf, svs, mods] } .set{ normal_bams_germlinevcf } + + normal_bams_germlinevcf.view() // normal_bams -> meta: [id, paired_data, platform, sex, type, fiber, basecall_model] // bam: list of concatenated aligned bams @@ -175,6 +182,7 @@ workflow TUMOR_NORMAL_HAPPHASE { } .mix(normal_bams) .set{ mixed_bams_vcf } + mixed_bams_vcf.view() // mixed_bams_vcf -> meta: [id, paired_data, platform, sex, type, fiber, basecall_model] // bam: list of concatenated aligned bams // bai: indexes for bam files @@ -267,6 +275,8 @@ workflow TUMOR_NORMAL_HAPPHASE { // MODULE: CLAIRS // + clairs_input.view() + CLAIRS ( clairs_input, fasta, From 0d11cb92a2b88bd6c19c57d6d75c124072895f61 Mon Sep 17 00:00:00 2001 From: robert-a-forsyth Date: Thu, 27 Nov 2025 13:58:31 +0100 Subject: [PATCH 32/42] fix multichannel --- subworkflows/local/tumor_normal_happhase.nf | 2 +- tests/default.nf.test.snap | 366 +------------------- 2 files changed, 6 insertions(+), 362 deletions(-) diff --git a/subworkflows/local/tumor_normal_happhase.nf b/subworkflows/local/tumor_normal_happhase.nf index f5326742..2b987254 100644 --- a/subworkflows/local/tumor_normal_happhase.nf +++ b/subworkflows/local/tumor_normal_happhase.nf @@ -30,7 +30,6 @@ workflow TUMOR_NORMAL_HAPPHASE { } .set{ mixed_bams } - mixed_bams.view() // Get normal bams and add platform/model info for Clair3 usage // remove type from so that information can be merged easier later @@ -182,6 +181,7 @@ workflow TUMOR_NORMAL_HAPPHASE { } .mix(normal_bams) .set{ mixed_bams_vcf } + mixed_bams_vcf.view() // mixed_bams_vcf -> meta: [id, paired_data, platform, sex, type, fiber, basecall_model] // bam: list of concatenated aligned bams diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 52651ce4..c422d2b8 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -1,375 +1,19 @@ { "-profile test": { "content": [ - 82, - { - "BCFTOOLS_CONCAT": { - "bcftools": 1.22 - }, - "BCFTOOLS_SORT": { - "bcftools": 1.22 - }, - "CLAIR3": { - "clair3": "1.2.0" - }, - "CLAIRS": { - "clairs": "0.4.1" - }, - "CLAIRSTO": { - "clairsto": "0.4.0" - }, - "CRAMINO_POST": { - "cramino": "1.0.0" - }, - "CRAMINO_PRE": { - "cramino": "1.0.0" - }, - "GERMLINE_VEP": { - "ensemblvep": 114.2, - "tabix": 1.21 - }, - "LONGPHASE_HAPLOTAG": { - "longphase": "1.7.3" - }, - "LONGPHASE_PHASE": { - "longphase": "1.7.3" - }, - "METAEXTRACT": { - "samtools": 1.21 - }, - "MINIMAP2_ALIGN": { - "minimap2": "2.29-r1283", - "samtools": 1.21 - }, - "MOSDEPTH": { - "mosdepth": "0.3.10" - }, - "SAMTOOLS_FAIDX": { - "samtools": 1.21 - }, - "SAMTOOLS_FLAGSTAT": { - "samtools": 1.21 - }, - "SAMTOOLS_IDXSTATS": { - "samtools": 1.21 - }, - "SAMTOOLS_INDEX": { - "samtools": 1.21 - }, - "SAMTOOLS_STATS": { - "samtools": 1.21 - }, - "SEVERUS": { - "severus": 1.6 - }, - "SOMATIC_VEP": { - "ensemblvep": 114.2, - "tabix": 1.21 - }, - "SV_VEP": { - "ensemblvep": 114.2, - "tabix": 1.21 - }, - "UNTAR": { - "untar": 1.34 - }, - "UNZIP_FASTA": { - "pigz": 2.8 - }, - "VCFSPLIT": { - "vcfsplit": 1.2 - }, - "WGET": { - "wget": "1.21.4" - }, - "Workflow": { - "IntGenomicsLab/lrsomatic": "v1.0.0dev" - } - }, + 0, + null, [ - "multiqc", - "multiqc/multiqc_data", - "multiqc/multiqc_data/BETA-multiqc.parquet", - "multiqc/multiqc_data/llms-full.txt", - "multiqc/multiqc_data/mosdepth-coverage-per-contig-single.txt", - "multiqc/multiqc_data/mosdepth-cumcoverage-dist-id.txt", - "multiqc/multiqc_data/mosdepth_cov_dist.txt", - "multiqc/multiqc_data/mosdepth_cumcov_dist.txt", - "multiqc/multiqc_data/mosdepth_perchrom.txt", - 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644f5aac..dd3d074b 100644 --- a/subworkflows/local/tumor_only_happhase.nf +++ b/subworkflows/local/tumor_only_happhase.nf @@ -22,7 +22,6 @@ workflow TUMOR_ONLY_HAPPHASE { tumor_only_severus = Channel.empty() somatic_vep = Channel.empty() germline_vep = Channel.empty() - tumor_bams.view() tumor_bams .map{ meta, bam, bai -> def clairSTO_model = (!meta.clairSTO_model || meta.clairSTO_model.toString().trim() in ['', '[]']) ? clairSTO_modelMap.get(meta.basecall_model.toString().trim()) : meta.clairSTO_model @@ -30,7 +29,6 @@ workflow TUMOR_ONLY_HAPPHASE { } .set{ tumor_bams } - tumor_bams.view() // // MODULE: CLAIRSTO From 800064f54efc30bf29a59be2547dd81dcc87c591 Mon Sep 17 00:00:00 2001 From: robert-a-forsyth Date: Thu, 27 Nov 2025 14:25:12 +0100 Subject: [PATCH 34/42] change channel --- subworkflows/local/tumor_normal_happhase.nf | 3 +++ 1 file changed, 3 insertions(+) diff --git a/subworkflows/local/tumor_normal_happhase.nf b/subworkflows/local/tumor_normal_happhase.nf index 2b987254..e99e81b2 100644 --- a/subworkflows/local/tumor_normal_happhase.nf +++ b/subworkflows/local/tumor_normal_happhase.nf @@ -104,6 +104,7 @@ workflow TUMOR_NORMAL_HAPPHASE { fai ) + CLAIR3.out.vcf.view() ch_versions = ch_versions.mix(CLAIR3.out.versions) // Add germline vcf to normal bams @@ -134,6 +135,8 @@ workflow TUMOR_NORMAL_HAPPHASE { } .set { germline_vep } + germline_vep.view() + // // MODULE: LONGPHASE_PHASE // From be9e0ea0a18e9cfbe235d7d6a4a5c2b539aac2a6 Mon Sep 17 00:00:00 2001 From: robert-a-forsyth Date: Thu, 27 Nov 2025 15:08:38 +0100 Subject: [PATCH 35/42] remove view --- subworkflows/local/tumor_normal_happhase.nf | 8 -------- 1 file changed, 8 deletions(-) diff --git a/subworkflows/local/tumor_normal_happhase.nf b/subworkflows/local/tumor_normal_happhase.nf index e99e81b2..678f1cd6 100644 --- a/subworkflows/local/tumor_normal_happhase.nf +++ b/subworkflows/local/tumor_normal_happhase.nf @@ -56,7 +56,6 @@ workflow TUMOR_NORMAL_HAPPHASE { } .set { normal_bams_model } - normal_bams_model.view() normal_bams_model .combine(downloaded_model_files,by:0) @@ -66,7 +65,6 @@ workflow TUMOR_NORMAL_HAPPHASE { } .set{ normal_bams } - normal_bams.view() // normal_bams -> meta: [id, paired_data, platform, sex, fiber, basecall_model] // bam: list of concatenated aligned bams // bai: indexes for bam files @@ -89,7 +87,6 @@ workflow TUMOR_NORMAL_HAPPHASE { } .set{ tumor_bams } - tumor_bams.view() // tumor_bams -> meta: [id, paired_data, platform, sex, fiber, basecall_model] // bam: list of concatenated aligned bams // bai: indexes for bam files @@ -104,7 +101,6 @@ workflow TUMOR_NORMAL_HAPPHASE { fai ) - CLAIR3.out.vcf.view() ch_versions = ch_versions.mix(CLAIR3.out.versions) // Add germline vcf to normal bams @@ -119,7 +115,6 @@ workflow TUMOR_NORMAL_HAPPHASE { } .set{ normal_bams_germlinevcf } - normal_bams_germlinevcf.view() // normal_bams -> meta: [id, paired_data, platform, sex, type, fiber, basecall_model] // bam: list of concatenated aligned bams @@ -135,7 +130,6 @@ workflow TUMOR_NORMAL_HAPPHASE { } .set { germline_vep } - germline_vep.view() // // MODULE: LONGPHASE_PHASE @@ -185,7 +179,6 @@ workflow TUMOR_NORMAL_HAPPHASE { .mix(normal_bams) .set{ mixed_bams_vcf } - mixed_bams_vcf.view() // mixed_bams_vcf -> meta: [id, paired_data, platform, sex, type, fiber, basecall_model] // bam: list of concatenated aligned bams // bai: indexes for bam files @@ -278,7 +271,6 @@ workflow TUMOR_NORMAL_HAPPHASE { // MODULE: CLAIRS // - clairs_input.view() CLAIRS ( clairs_input, From 67f4be663a45d8119eaf14e46a9972bfe9ff6179 Mon Sep 17 00:00:00 2001 From: robert-a-forsyth Date: Thu, 27 Nov 2025 15:35:02 +0100 Subject: [PATCH 36/42] lint and snapshot --- modules.json | 115 +++--------- tests/default.nf.test.snap | 366 ++++++++++++++++++++++++++++++++++++- 2 files changed, 390 insertions(+), 91 deletions(-) diff --git a/modules.json b/modules.json index 4afad53b..58f3aae4 100644 --- a/modules.json +++ b/modules.json @@ -8,178 +8,129 @@ "ascat": { "branch": "master", "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/ascat/ascat.diff" }, "bcftools/concat": { "branch": "master", "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726", - "installed_by": [ - "modules", - "vcf_gather_bcftools" - ] + "installed_by": ["modules", "vcf_gather_bcftools"] }, "bcftools/merge": { "branch": "master", "git_sha": "f17049e03697726ace7499d2fe342f892594f6f3", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/sort": { "branch": "master", "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726", - "installed_by": [ - "vcf_gather_bcftools" - ], + "installed_by": ["vcf_gather_bcftools"], "patch": "modules/nf-core/bcftools/sort/bcftools-sort.diff" }, "ensemblvep/download": { "branch": "master", "git_sha": "2fcc53751152a999bfc9c24f75f494b9e5bb338f", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "ensemblvep/vep": { "branch": "master", "git_sha": "48ca3de1737b0144aa9fe05bea2b681f0ae45a95", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff" }, "longphase/haplotag": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "longphase/phase": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/longphase/phase/longphase-phase.diff" }, "minimap2/align": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/minimap2/align/minimap2-align.diff" }, "minimap2/index": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, 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"branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "bam_stats_samtools" - ] + "installed_by": ["bam_stats_samtools"] }, "samtools/idxstats": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "bam_stats_samtools" - ] + "installed_by": ["bam_stats_samtools"] }, "samtools/index": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/stats": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "bam_stats_samtools" - ], + "installed_by": ["bam_stats_samtools"], "patch": "modules/nf-core/samtools/stats/samtools-stats.diff" }, "severus": { "branch": "master", "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/severus/severus.diff" }, "untar": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "unzip": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "wget": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] } } }, @@ -188,33 +139,25 @@ "bam_stats_samtools": { "branch": "master", "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nextflow_pipeline": { "branch": "master", "git_sha": "c2b22d85f30a706a3073387f30380704fcae013b", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "51ae5406a030d4da1e49e4dab49756844fdd6c7a", - "installed_by": [ - "subworkflows" - ] + "installed_by": 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"sample3/variants/severus/read_ids.csv", + "sample3/variants/severus/read_qual.txt", + "sample3/variants/severus/severus.log", + "sample3/variants/severus/somatic_SVs", + "sample3/variants/severus/somatic_SVs/breakpoint_clusters.tsv", + "sample3/variants/severus/somatic_SVs/breakpoint_clusters_list.tsv", + "sample3/variants/severus/somatic_SVs/severus_somatic.vcf.gz", + "sample3/variants/severus/somatic_SVs/severus_somatic.vcf.gz.tbi", + "sample3/vep", + "sample3/vep/SVs", + "sample3/vep/SVs/sample3_SV_VEP.vcf.gz", + "sample3/vep/SVs/sample3_SV_VEP.vcf.gz.tbi", + "sample3/vep/SVs/sample3_SV_VEP.vcf.gz_summary.html", + "sample3/vep/germline", + "sample3/vep/germline/sample3_GERMLINE_VEP.vcf.gz", + "sample3/vep/germline/sample3_GERMLINE_VEP.vcf.gz.tbi", + "sample3/vep/germline/sample3_GERMLINE_VEP.vcf.gz_summary.html", + "sample3/vep/somatic", + "sample3/vep/somatic/sample3_SOMATIC_VEP.vcf.gz", + "sample3/vep/somatic/sample3_SOMATIC_VEP.vcf.gz.tbi", + "sample3/vep/somatic/sample3_SOMATIC_VEP.vcf.gz_summary.html" ], [ - + "sample1_normal.bam:md5,7373f28eae1e18614bec4508e6647ff2", + "sample1_normal.bam.bai:md5,fc9dd46a2a04c098cee87650edec0f89", + "sample1_tumor.bam:md5,4aa78492fa890945efe2af47cbe76194", + "sample1_tumor.bam.bai:md5,75ed8b553427bbbd9bbc3c7b52982e85", + "sample1.mosdepth.global.dist.txt:md5,4e1c72f8465c18ffd854c42850eb7c5f", + "sample1.mosdepth.summary.txt:md5,cf13d4b24e5ebf31b629a1195a1fff41", + "sample1.flagstat:md5,815a5385bd57ef44847714130b80d630", + "sample1.idxstats:md5,19be02d7e966e4a291b66ab5b14742d3", + "sample1.stats:md5,f61e05f232d4b3174797d4b25bdd9457", + "sample1.mosdepth.global.dist.txt:md5,e04da37ef2b7cd587fa3158b9f36d2cb", + "sample1.mosdepth.summary.txt:md5,ef3aefa72ca2e9bbbe5acc91fc1ecde6", + "sample1.flagstat:md5,34e851b5504d961632f26991160ded5a", + "sample1.idxstats:md5,1d43b03114bcc9b70d4333e91498efbe", + "sample1.stats:md5,afdcefd9c5a69d5252fe0f9186d349fd", + "breakpoint_clusters.tsv:md5,d36a70de292ee130ef30da4a58bced18", + "breakpoint_clusters_list.tsv:md5,0c0ce62e329f8de492487e8414c30a50", + "breakpoints_double.csv:md5,244b62ee8500ddccf63bf1a8eb19d7bf", + "read_qual.txt:md5,1ad9d1900f8dcb291c97adc65c9d341c", + "breakpoint_clusters.tsv:md5,d36a70de292ee130ef30da4a58bced18", + "breakpoint_clusters_list.tsv:md5,0c0ce62e329f8de492487e8414c30a50", + "sample2_normal.bam:md5,c96d49ed1176c787752e7fcf23bd5ffb", + "sample2_normal.bam.bai:md5,87d97a08bdca08f6eaf2725dd114d3c3", + "sample2_tumor.bam:md5,4f375cb01fb7a7c8161474f2f789d8a4", + "sample2_tumor.bam.bai:md5,54967d76febdeb0abed1bd68d8aee337", + "sample2.mosdepth.global.dist.txt:md5,6cdc97a81a603db702cb5a113b8bc62a", + "sample2.mosdepth.summary.txt:md5,864370930ec1d695d942f4960bcf8fc6", + "sample2.flagstat:md5,cce0bb7ca79e14d8369ccc714adf4be3", + "sample2.idxstats:md5,e7de97b2362a8e944896dc4eca0b0bd8", + "sample2.stats:md5,9d98e3ec064b376880648a79c199b9b5", + "sample2.mosdepth.global.dist.txt:md5,eda3bf93b39e342e85e43931ce8b417e", + "sample2.mosdepth.summary.txt:md5,a68ca9504f5c9b73bf697d8ac22a1df0", + "sample2.flagstat:md5,83e7d7d922941691d2b023f0bd9655aa", + "sample2.idxstats:md5,fe8a5d1263481ea7902d575b4d95f655", + "sample2.stats:md5,2904de743414042e112d541ffc0f83ba", + "breakpoint_clusters.tsv:md5,d36a70de292ee130ef30da4a58bced18", + "breakpoint_clusters_list.tsv:md5,0c0ce62e329f8de492487e8414c30a50", + "breakpoints_double.csv:md5,6a1d4530feae8258a925d1f0641a63ff", + "read_qual.txt:md5,27edf87814aec6fa18546c8606aae4ed", + "breakpoint_clusters.tsv:md5,d36a70de292ee130ef30da4a58bced18", + "breakpoint_clusters_list.tsv:md5,0c0ce62e329f8de492487e8414c30a50", + "sample3_tumor.bam:md5,c80bbdcb0a6fcfe4164c6d96e6d9ad6a", + "sample3_tumor.bam.bai:md5,cdf45221635a6b03be6f28aa60b202bc", + "sample3.mosdepth.global.dist.txt:md5,e04da37ef2b7cd587fa3158b9f36d2cb", + "sample3.mosdepth.summary.txt:md5,ef3aefa72ca2e9bbbe5acc91fc1ecde6", + "sample3.flagstat:md5,34e851b5504d961632f26991160ded5a", + "sample3.idxstats:md5,1d43b03114bcc9b70d4333e91498efbe", + "sample3.stats:md5,48eb55e610bd2a6d13c5d38d3c61d29e", + "breakpoint_clusters.tsv:md5,d36a70de292ee130ef30da4a58bced18", + "breakpoint_clusters_list.tsv:md5,0c0ce62e329f8de492487e8414c30a50", + "breakpoints_double.csv:md5,298a01c868eb493baaaa90ced9a9f17e", + "read_qual.txt:md5,1b4392f3b9071533e9ea77ff9df6c813", + "breakpoint_clusters.tsv:md5,d36a70de292ee130ef30da4a58bced18", + "breakpoint_clusters_list.tsv:md5,0c0ce62e329f8de492487e8414c30a50" ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-27T13:57:32.181376744" + "timestamp": "2025-11-27T15:31:19.623058622" } } \ No newline at end of file From 4b47c2f124ec9af142b60131c22d15493fd5af1f Mon Sep 17 00:00:00 2001 From: robert-a-forsyth Date: Thu, 27 Nov 2025 15:59:16 +0100 Subject: [PATCH 37/42] fix lint and snap --- lint_log.txt | 3596 +++++++++++++++++++ subworkflows/local/tumor_normal_happhase.nf | 6 +- 2 files changed, 3599 insertions(+), 3 deletions(-) create mode 100644 lint_log.txt diff --git a/lint_log.txt b/lint_log.txt new file mode 100644 index 00000000..5e087cd0 --- /dev/null +++ b/lint_log.txt @@ -0,0 +1,3596 @@ +[2025-11-27 15:47:39,242] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:47:39,244] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/lustre1/project/stg_00096/home/rforsyth/LRSomatic/lrsomatic, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:47:39,250] nf_core.utils [DEBUG ] Got '.' as path +[2025-11-27 15:47:39,251] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json +[2025-11-27 15:47:39,252] nf_core.utils [DEBUG ] Using config file: .nf-core.yml +[2025-11-27 15:47:39,252] nf_core.utils [DEBUG ] Got '.' as path +[2025-11-27 15:47:39,252] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json +[2025-11-27 15:47:39,254] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:47:39,258] git.cmd [DEBUG ] Popen(['git', 'version'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:47:39,260] git.cmd [DEBUG ] Popen(['git', 'fetch', '-v', '--progress', '--', 'origin'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=True) +[2025-11-27 15:47:40,027] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:47:40,360] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:47:40,375] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:47:40,376] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:47:40,376] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:47:40,378] nf_core.utils [DEBUG ] Got '.' as path +[2025-11-27 15:47:40,379] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json +[2025-11-27 15:47:40,379] nf_core.utils [DEBUG ] Using config file: .nf-core.yml +[2025-11-27 15:47:41,648] nf_core.pipelines.lint_utils [DEBUG ] The following files were modified by prettier: + +modules.json + + +[2025-11-27 15:47:41,651] nf_core.utils [DEBUG ] Got '.' as path +[2025-11-27 15:47:41,651] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json +[2025-11-27 15:47:41,652] nf_core.components.lint [DEBUG ] Registry set to quay.io +[2025-11-27 15:47:41,652] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:47:41,653] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:47:41,705] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:47:41,724] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:47:41,724] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:47:41,725] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:47:41,727] nf_core.utils [DEBUG ] Got '.' as path +[2025-11-27 15:47:41,727] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json +[2025-11-27 15:47:41,728] nf_core.utils [DEBUG ] Using config file: .nf-core.yml +[2025-11-27 15:47:42,155] nf_core.pipelines.lint_utils [DEBUG ] The following files were modified by prettier: + +modules.json + + +[2025-11-27 15:47:42,157] nf_core.utils [DEBUG ] Got '.' as path +[2025-11-27 15:47:42,157] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json +[2025-11-27 15:47:42,158] nf_core.components.lint [DEBUG ] Registry set to quay.io +[2025-11-27 15:47:42,160] nf_core.utils [DEBUG ] Got '.' as path +[2025-11-27 15:47:42,160] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json +[2025-11-27 15:47:42,160] nf_core.utils [DEBUG ] Using config file: .nf-core.yml +[2025-11-27 15:47:42,162] nf_core.utils [DEBUG ] Got '.' as path +[2025-11-27 15:47:42,162] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json +[2025-11-27 15:47:42,163] nf_core.utils [DEBUG ] Using config file: .nf-core.yml +[2025-11-27 15:47:42,163] nf_core.pipelines.lint [INFO ] Testing pipeline: [magenta]. +[2025-11-27 15:47:42,165] nf_core.pipelines.lint [DEBUG ] Running lint test: files_exist +[2025-11-27 15:47:42,167] nf_core.pipelines.lint [DEBUG ] Running lint test: nextflow_config +[2025-11-27 15:47:42,169] nf_core.utils [DEBUG ] Got '.' as path +[2025-11-27 15:47:42,169] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json +[2025-11-27 15:47:42,170] nf_core.utils [DEBUG ] Using config file: .nf-core.yml +[2025-11-27 15:47:42,171] nf_core.utils [DEBUG ] Got '.' as path +[2025-11-27 15:47:42,171] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json +[2025-11-27 15:47:42,171] nf_core.pipelines.schema [DEBUG ] Ignoring parameters from config: ['genomes'] +[2025-11-27 15:47:42,171] nf_core.pipelines.schema [DEBUG ] Ignoring parameters: ['help', 'help_full', 'show_hidden', 'trace_report_suffix', 'genomes'] +[2025-11-27 15:47:42,172] nf_core.pipelines.schema [DEBUG ] JSON file loaded: nextflow_schema.json +[2025-11-27 15:47:42,172] nf_core.pipelines.lint [DEBUG ] Running lint test: nf_test_content +[2025-11-27 15:47:42,173] nf_core.utils [DEBUG ] Got '.' as path +[2025-11-27 15:47:42,174] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json +[2025-11-27 15:47:42,174] nf_core.utils [DEBUG ] Using config file: .nf-core.yml +[2025-11-27 15:47:42,175] nf_core.pipelines.lint [DEBUG ] Running lint test: files_unchanged +[2025-11-27 15:47:42,197] nf_core.utils [DEBUG ] Could not find a config file in the directory '/tmp/tmpu9m_99l5/IntGenomicsLab-lrsomatic' +[2025-11-27 15:47:42,378] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:47:42,378] nf_core.utils [DEBUG ] Could not find git hash for pipeline: /tmp/tmpu9m_99l5/IntGenomicsLab-lrsomatic. /tmp/tmpu9m_99l5/IntGenomicsLab-lrsomatic +[2025-11-27 15:47:42,378] nf_core.utils [DEBUG ] Got '/tmp/tmpu9m_99l5/IntGenomicsLab-lrsomatic' as path +[2025-11-27 15:47:42,378] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-2540e072f807b83f582a63138.json +[2025-11-27 15:47:42,379] nf_core.utils [DEBUG ] No conda `environment.yml` file found. +[2025-11-27 15:47:42,382] urllib3.connectionpool [DEBUG ] Starting new HTTPS connection (1): nf-co.re:443 +[2025-11-27 15:47:42,674] urllib3.connectionpool [DEBUG ] https://nf-co.re:443 "GET /pipelines.json HTTP/1.1" 200 None +[2025-11-27 15:47:42,909] nf_core.pipelines.rocrate [DEBUG ] Adding topics: ['nf-core', 'nextflow'] +[2025-11-27 15:47:42,909] nf_core.pipelines.rocrate [DEBUG ] No git repository found. No git contributors will be added as authors. +[2025-11-27 15:47:42,910] nf_core.pipelines.rocrate [INFO ] Saving metadata file to '/tmp/tmpu9m_99l5/IntGenomicsLab-lrsomatic' +[2025-11-27 15:47:42,911] nf_core.utils [DEBUG ] Got '/tmp/tmpu9m_99l5/IntGenomicsLab-lrsomatic' as path +[2025-11-27 15:47:42,911] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-2540e072f807b83f582a63138.json +[2025-11-27 15:47:42,911] nf_core.utils [DEBUG ] Using config file: /tmp/tmpu9m_99l5/IntGenomicsLab-lrsomatic/.nf-core.yml +[2025-11-27 15:47:42,914] nf_core.utils [DEBUG ] Got '/tmp/tmpu9m_99l5/IntGenomicsLab-lrsomatic' as path +[2025-11-27 15:47:42,914] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-2540e072f807b83f582a63138.json +[2025-11-27 15:47:42,915] nf_core.utils [DEBUG ] Using config file: /tmp/tmpu9m_99l5/IntGenomicsLab-lrsomatic/.nf-core.yml +[2025-11-27 15:47:43,547] nf_core.pipelines.lint_utils [DEBUG ] prettier.................................................................Passed + +[2025-11-27 15:47:43,550] nf_core.pipelines.lint [DEBUG ] Running lint test: actions_nf_test +[2025-11-27 15:47:43,556] nf_core.pipelines.lint [DEBUG ] Running lint test: actions_awstest +[2025-11-27 15:47:43,556] nf_core.pipelines.lint [DEBUG ] Running lint test: actions_awsfulltest +[2025-11-27 15:47:43,556] nf_core.pipelines.lint [DEBUG ] Running lint test: readme +[2025-11-27 15:47:43,557] nf_core.pipelines.lint [DEBUG ] Running lint test: pipeline_todos +[2025-11-27 15:47:43,708] nf_core.pipelines.lint [DEBUG ] Running lint test: pipeline_if_empty_null +[2025-11-27 15:50:35,955] nf_core.pipelines.lint [DEBUG ] Running lint test: plugin_includes +[2025-11-27 15:50:35,958] nf_core.pipelines.lint [DEBUG ] Running lint test: pipeline_name_conventions +[2025-11-27 15:50:35,959] nf_core.pipelines.lint [DEBUG ] Running lint test: template_strings +[2025-11-27 15:50:36,008] nf_core.pipelines.lint [DEBUG ] Running lint test: schema_lint +[2025-11-27 15:50:36,008] nf_core.utils [DEBUG ] Got '.' as path +[2025-11-27 15:50:36,009] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json +[2025-11-27 15:50:36,042] nf_core.utils [DEBUG ] Got '.' as path +[2025-11-27 15:50:36,042] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json +[2025-11-27 15:50:36,043] nf_core.pipelines.lint [DEBUG ] Skipping lint test 'schema_params' +[2025-11-27 15:50:36,043] nf_core.pipelines.lint [DEBUG ] Running lint test: system_exit +[2025-11-27 15:50:36,093] nf_core.pipelines.lint [DEBUG ] Running lint test: schema_description +[2025-11-27 15:50:36,093] nf_core.utils [DEBUG ] Got '.' as path +[2025-11-27 15:50:36,093] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json +[2025-11-27 15:50:36,094] nf_core.utils [DEBUG ] Got '.' as path +[2025-11-27 15:50:36,094] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json +[2025-11-27 15:50:36,125] nf_core.pipelines.lint [DEBUG ] Running lint test: actions_schema_validation +[2025-11-27 15:50:36,126] urllib3.connectionpool [DEBUG ] Starting new HTTPS connection (1): www.schemastore.org:443 +[2025-11-27 15:50:36,292] urllib3.connectionpool [DEBUG ] https://www.schemastore.org:443 "GET /github-workflow HTTP/1.1" 200 14042 +[2025-11-27 15:50:36,454] nf_core.pipelines.lint [DEBUG ] Running lint test: merge_markers +[2025-11-27 15:50:36,514] nf_core.pipelines.lint [DEBUG ] Running lint test: modules_json +[2025-11-27 15:50:36,514] nf_core.pipelines.lint [DEBUG ] Running lint test: multiqc_config +[2025-11-27 15:50:36,516] nf_core.utils [DEBUG ] Got '.' as path +[2025-11-27 15:50:36,516] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json +[2025-11-27 15:50:36,517] nf_core.utils [DEBUG ] Using config file: .nf-core.yml +[2025-11-27 15:50:36,517] nf_core.pipelines.lint [DEBUG ] Running lint test: modules_structure +[2025-11-27 15:50:36,520] nf_core.pipelines.lint [DEBUG ] Running lint test: local_component_structure +[2025-11-27 15:50:36,520] nf_core.pipelines.lint [DEBUG ] Running lint test: base_config +[2025-11-27 15:50:36,522] nf_core.utils [DEBUG ] Got '.' as path +[2025-11-27 15:50:36,522] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json +[2025-11-27 15:50:36,522] nf_core.utils [DEBUG ] Using config file: .nf-core.yml +[2025-11-27 15:50:36,522] nf_core.pipelines.lint.configs [DEBUG ] found sections: [] +[2025-11-27 15:50:36,539] nf_core.pipelines.lint.configs [DEBUG ] found nf_files: ['main.nf', 'workflows/lrsomatic.nf', 'subworkflows/local/tumor_normal_happhase.nf', 'subworkflows/local/tumor_only_happhase.nf', 'subworkflows/local/prepare_annotation.nf', 'subworkflows/local/prepare_reference_files.nf', 'subworkflows/nf-core/utils_nfschema_plugin/main.nf', 'subworkflows/nf-core/bam_stats_samtools/main.nf', 'subworkflows/nf-core/utils_nextflow_pipeline/main.nf', 'subworkflows/nf-core/utils_nfcore_pipeline/main.nf', 'subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf', 'modules/nf-core/ascat/main.nf', 'modules/nf-core/mosdepth/main.nf', 'modules/nf-core/multiqc/main.nf', 'modules/nf-core/wget/main.nf', 'modules/nf-core/unzip/main.nf', 'modules/nf-core/untar/main.nf', 'modules/nf-core/severus/main.nf', 'modules/nf-core/minimap2/align/main.nf', 'modules/nf-core/minimap2/index/main.nf', 'modules/nf-core/bcftools/merge/main.nf', 'modules/nf-core/bcftools/sort/main.nf', 'modules/nf-core/bcftools/concat/main.nf', 'modules/nf-core/modkit/pileup/main.nf', 'modules/nf-core/samtools/idxstats/main.nf', 'modules/nf-core/samtools/faidx/main.nf', 'modules/nf-core/samtools/cat/main.nf', 'modules/nf-core/samtools/index/main.nf', 'modules/nf-core/samtools/stats/main.nf', 'modules/nf-core/samtools/flagstat/main.nf', 'modules/nf-core/longphase/haplotag/main.nf', 'modules/nf-core/longphase/phase/main.nf', 'modules/nf-core/ensemblvep/vep/main.nf', 'modules/nf-core/ensemblvep/download/main.nf', 'modules/nf-core/pigz/uncompress/main.nf', 'modules/local/wakhan/main.nf', 'modules/local/clairs/main.nf', 'modules/local/cramino/main.nf', 'modules/local/metaextract/main.nf', 'modules/local/clairsto/main.nf', 'modules/local/vcfsplit/main.nf', 'modules/local/clair3/main.nf', 'modules/local/fibertoolsrs/fire/main.nf', 'modules/local/fibertoolsrs/predictm6a/main.nf', 'modules/local/fibertoolsrs/qc/main.nf', 'modules/local/fibertoolsrs/nucleosomes/main.nf'] +[2025-11-27 15:50:36,539] nf_core.pipelines.lint [DEBUG ] Running lint test: modules_config +[2025-11-27 15:50:36,541] nf_core.utils [DEBUG ] Got '.' as path +[2025-11-27 15:50:36,541] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json +[2025-11-27 15:50:36,542] nf_core.utils [DEBUG ] Using config file: .nf-core.yml +[2025-11-27 15:50:36,542] nf_core.pipelines.lint.configs [DEBUG ] found sections: ['ENSEMBLVEP_DOWNLOAD'] +[2025-11-27 15:50:36,558] nf_core.pipelines.lint.configs [DEBUG ] found nf_files: ['main.nf', 'workflows/lrsomatic.nf', 'subworkflows/local/tumor_normal_happhase.nf', 'subworkflows/local/tumor_only_happhase.nf', 'subworkflows/local/prepare_annotation.nf', 'subworkflows/local/prepare_reference_files.nf', 'subworkflows/nf-core/utils_nfschema_plugin/main.nf', 'subworkflows/nf-core/bam_stats_samtools/main.nf', 'subworkflows/nf-core/utils_nextflow_pipeline/main.nf', 'subworkflows/nf-core/utils_nfcore_pipeline/main.nf', 'subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf', 'modules/nf-core/ascat/main.nf', 'modules/nf-core/mosdepth/main.nf', 'modules/nf-core/multiqc/main.nf', 'modules/nf-core/wget/main.nf', 'modules/nf-core/unzip/main.nf', 'modules/nf-core/untar/main.nf', 'modules/nf-core/severus/main.nf', 'modules/nf-core/minimap2/align/main.nf', 'modules/nf-core/minimap2/index/main.nf', 'modules/nf-core/bcftools/merge/main.nf', 'modules/nf-core/bcftools/sort/main.nf', 'modules/nf-core/bcftools/concat/main.nf', 'modules/nf-core/modkit/pileup/main.nf', 'modules/nf-core/samtools/idxstats/main.nf', 'modules/nf-core/samtools/faidx/main.nf', 'modules/nf-core/samtools/cat/main.nf', 'modules/nf-core/samtools/index/main.nf', 'modules/nf-core/samtools/stats/main.nf', 'modules/nf-core/samtools/flagstat/main.nf', 'modules/nf-core/longphase/haplotag/main.nf', 'modules/nf-core/longphase/phase/main.nf', 'modules/nf-core/ensemblvep/vep/main.nf', 'modules/nf-core/ensemblvep/download/main.nf', 'modules/nf-core/pigz/uncompress/main.nf', 'modules/local/wakhan/main.nf', 'modules/local/clairs/main.nf', 'modules/local/cramino/main.nf', 'modules/local/metaextract/main.nf', 'modules/local/clairsto/main.nf', 'modules/local/vcfsplit/main.nf', 'modules/local/clair3/main.nf', 'modules/local/fibertoolsrs/fire/main.nf', 'modules/local/fibertoolsrs/predictm6a/main.nf', 'modules/local/fibertoolsrs/qc/main.nf', 'modules/local/fibertoolsrs/nucleosomes/main.nf'] +[2025-11-27 15:50:36,559] nf_core.pipelines.lint [DEBUG ] Running lint test: nfcore_yml +[2025-11-27 15:50:36,563] nf_core.pipelines.lint [DEBUG ] Running lint test: rocrate_readme_sync +[2025-11-27 15:50:36,566] nf_core.components.nfcore_component [DEBUG ] Found 2 inputs in modules/local/wakhan/main.nf +[2025-11-27 15:50:36,566] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'tumor_input': {}}, {'tumor_index': {}}, {'normal_input': {}}, {'normal_index': {}}, {'vcf': {}}, {'breakpoints': {}}], [{'meta2': {}}, {'reference': {}}]] +[2025-11-27 15:50:36,566] nf_core.components.nfcore_component [DEBUG ] Found output_data: + tuple val(meta), path("*/*_genes_genome.html") , emit: genes_genome_html + tuple val(meta), path("*/*_genes_genome.pdf") , emit: genes_genome_pdf + tuple val(meta), path("*/*_genome_copynumbers_breakpoints.html") , emit: breakpoints_html + tuple val(meta), path("*/*_genome_copynumbers_breakpoints.pdf") , emit: breakpoints_pdf + tuple val(meta), path("*/*_genome_copynumbers_breakpoints_subclonal.html") , emit: breakpoints_subclonal_html + tuple val(meta), path("*/*_genome_copynumbers_breakpoints_subclonal.pdf") , emit: breakpoints_subclonal_pdf + tuple val(meta), path("*/*_genome_copynumbers_details.html") , emit: copynumbers_details_html + tuple val(meta), path("*/*_genome_copynumbers_details.pdf") , emit: copynumbers_details_pdf + tuple val(meta), path("*/bed_output/*.bed") , emit: bed_files + tuple val(meta), path("*/variation_plots/*.html") , emit: variation_plots + tuple val(meta), path("*/vcf_output/*_wakhan_cna_*.vcf") , emit: vcf_files + tuple val(meta), path("*_heatmap_ploidy_purity.html") , emit: heatmap_html + tuple val(meta), path("*_heatmap_ploidy_purity.html.pdf") , emit: heatmap_pdf + tuple val(meta), path("*_optimized_peak.html") , emit: optimized_peak_html + tuple val(meta), path("coverage_data/*.csv") , emit: coverage_csv + tuple val(meta), path("coverage_plots/*.html") , emit: coverage_plots_html + tuple val(meta), path("coverage_plots/*.pdf") , emit: coverage_plots_pdf + tuple val(meta), path("phasing_output/*.html") , emit: phasing_html + tuple val(meta), path("phasing_output/*.pdf") , emit: phasing_pdf + tuple val(meta), path("phasing_output/*.rephased.vcf.gz") , emit: rephased_vcf + tuple val(meta), path("phasing_output/*.rephased.vcf.gz.csi") , emit: rephased_vcf_index + tuple val(meta), path("snps_loh_plots/*_genome_snps_ratio_loh.html") , emit: snps_loh_plot, optional: true + tuple val(meta), path("solutions_ranks.tsv") , emit: solutions_ranks + path "versions.yml" , emit: versions + + +[2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Found 24 outputs in modules/local/wakhan/main.nf +[2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Outputs: {'genes_genome_html': [[{'meta': {}}, {'*/*_genes_genome.html': {}}]], 'genes_genome_pdf': [[{'meta': {}}, {'*/*_genes_genome.pdf': {}}]], 'breakpoints_html': [[{'meta': {}}, {'*/*_genome_copynumbers_breakpoints.html': {}}]], 'breakpoints_pdf': [[{'meta': {}}, {'*/*_genome_copynumbers_breakpoints.pdf': {}}]], 'breakpoints_subclonal_html': [[{'meta': {}}, {'*/*_genome_copynumbers_breakpoints_subclonal.html': {}}]], 'breakpoints_subclonal_pdf': [[{'meta': {}}, {'*/*_genome_copynumbers_breakpoints_subclonal.pdf': {}}]], 'copynumbers_details_html': [[{'meta': {}}, {'*/*_genome_copynumbers_details.html': {}}]], 'copynumbers_details_pdf': [[{'meta': {}}, {'*/*_genome_copynumbers_details.pdf': {}}]], 'bed_files': [[{'meta': {}}, {'*/bed_output/*.bed': {}}]], 'variation_plots': [[{'meta': {}}, {'*/variation_plots/*.html': {}}]], 'vcf_files': [[{'meta': {}}, {'*/vcf_output/*_wakhan_cna_*.vcf': {}}]], 'heatmap_html': [[{'meta': {}}, {'*_heatmap_ploidy_purity.html': {}}]], 'heatmap_pdf': [[{'meta': {}}, {'*_heatmap_ploidy_purity.html.pdf': {}}]], 'optimized_peak_html': [[{'meta': {}}, {'*_optimized_peak.html': {}}]], 'coverage_csv': [[{'meta': {}}, {'coverage_data/*.csv': {}}]], 'coverage_plots_html': [[{'meta': {}}, {'coverage_plots/*.html': {}}]], 'coverage_plots_pdf': [[{'meta': {}}, {'coverage_plots/*.pdf': {}}]], 'phasing_html': [[{'meta': {}}, {'phasing_output/*.html': {}}]], 'phasing_pdf': [[{'meta': {}}, {'phasing_output/*.pdf': {}}]], 'rephased_vcf': [[{'meta': {}}, {'phasing_output/*.rephased.vcf.gz': {}}]], 'rephased_vcf_index': [[{'meta': {}}, {'phasing_output/*.rephased.vcf.gz.csi': {}}]], 'snps_loh_plot': [[{'meta': {}}, {'snps_loh_plots/*_genome_snps_ratio_loh.html': {}}]], 'solutions_ranks': [[{'meta': {}}, {'solutions_ranks.tsv': {}}]], 'versions': [{'versions.yml': {}}]} +[2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Output data: + tuple val(meta), path("*/*_genes_genome.html") , emit: genes_genome_html + tuple val(meta), path("*/*_genes_genome.pdf") , emit: genes_genome_pdf + tuple val(meta), path("*/*_genome_copynumbers_breakpoints.html") , emit: breakpoints_html + tuple val(meta), path("*/*_genome_copynumbers_breakpoints.pdf") , emit: breakpoints_pdf + tuple val(meta), path("*/*_genome_copynumbers_breakpoints_subclonal.html") , emit: breakpoints_subclonal_html + tuple val(meta), path("*/*_genome_copynumbers_breakpoints_subclonal.pdf") , emit: breakpoints_subclonal_pdf + tuple val(meta), path("*/*_genome_copynumbers_details.html") , emit: copynumbers_details_html + tuple val(meta), path("*/*_genome_copynumbers_details.pdf") , emit: copynumbers_details_pdf + tuple val(meta), path("*/bed_output/*.bed") , emit: bed_files + tuple val(meta), path("*/variation_plots/*.html") , emit: variation_plots + tuple val(meta), path("*/vcf_output/*_wakhan_cna_*.vcf") , emit: vcf_files + tuple val(meta), path("*_heatmap_ploidy_purity.html") , emit: heatmap_html + tuple val(meta), path("*_heatmap_ploidy_purity.html.pdf") , emit: heatmap_pdf + tuple val(meta), path("*_optimized_peak.html") , emit: optimized_peak_html + tuple val(meta), path("coverage_data/*.csv") , emit: coverage_csv + tuple val(meta), path("coverage_plots/*.html") , emit: coverage_plots_html + tuple val(meta), path("coverage_plots/*.pdf") , emit: coverage_plots_pdf + tuple val(meta), path("phasing_output/*.html") , emit: phasing_html + tuple val(meta), path("phasing_output/*.pdf") , emit: phasing_pdf + tuple val(meta), path("phasing_output/*.rephased.vcf.gz") , emit: rephased_vcf + tuple val(meta), path("phasing_output/*.rephased.vcf.gz.csi") , emit: rephased_vcf_index + tuple val(meta), path("snps_loh_plots/*_genome_snps_ratio_loh.html") , emit: snps_loh_plot, optional: true + tuple val(meta), path("solutions_ranks.tsv") , emit: solutions_ranks + path "versions.yml" , emit: versions + + +[2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/local/wakhan/main.nf +[2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Topics: {} +[2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Found 3 inputs in modules/local/clairs/main.nf +[2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'tumor_bam': {}}, {'tumor_bai': {}}, {'normal_bam': {}}, {'normal_bai': {}}, {'model': {}}], [{'meta2': {}}, {'reference': {}}], [{'meta3': {}}, {'index': {}}]] +[2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Found output_data: + tuple val(meta), path("*.vcf.gz"), emit: vcfs + tuple val(meta), path("*.vcf.gz.tbi"), emit: tbi + path "versions.yml", emit: versions + + +[2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Found 3 outputs in modules/local/clairs/main.nf +[2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Outputs: {'vcfs': [[{'meta': {}}, {'*.vcf.gz': {}}]], 'tbi': [[{'meta': {}}, {'*.vcf.gz.tbi': {}}]], 'versions': [{'versions.yml': {}}]} +[2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Output data: + tuple val(meta), path("*.vcf.gz"), emit: vcfs + tuple val(meta), path("*.vcf.gz.tbi"), emit: tbi + path "versions.yml", emit: versions + + +[2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/local/clairs/main.nf +[2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Topics: {} +[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/local/cramino/main.nf +[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'bam': {}}]] +[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Found output_data: + tuple val(meta), path("*.txt"), emit: txt + path "versions.yml" , emit: versions + + +[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/local/cramino/main.nf +[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Outputs: {'txt': [[{'meta': {}}, {'*.txt': {}}]], 'versions': [{'versions.yml': {}}]} +[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Output data: + tuple val(meta), path("*.txt"), emit: txt + path "versions.yml" , emit: versions + + +[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/local/cramino/main.nf +[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Topics: {} +[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/local/metaextract/main.nf +[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'bam': {}}]] +[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Found output_data: + tuple val(meta), env(basecall_model), env(kinetics) , emit: meta_ext + path "versions.yml" , emit: versions + + +[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/local/metaextract/main.nf +[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Outputs: {'meta_ext': [[{'meta': {}}, {'basecall_model': {}}, {'kinetics': {}}]], 'versions': [{'versions.yml': {}}]} +[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Output data: + tuple val(meta), env(basecall_model), env(kinetics) , emit: meta_ext + path "versions.yml" , emit: versions + + +[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/local/metaextract/main.nf +[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Topics: {} +[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Found 7 inputs in modules/local/clairsto/main.nf +[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'tumor_bam': {}}, {'tumor_bai': {}}, {'model': {}}], [{'meta2': {}}, {'reference': {}}], [{'meta3': {}}, {'index': {}}], {'dbSNP': {}}, {'colors': {}}, {'onekgenomes': {}}, {'gnomad': {}}] +[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Found output_data: + tuple val(meta), path("indel.vcf.gz"), emit: indel_vcf + tuple val(meta), path("indel.vcf.gz.tbi"), emit: indel_tbi + tuple val(meta), path("snv.vcf.gz"), emit: snv_vcf + tuple val(meta), path("snv.vcf.gz.tbi"), emit: snv_tbi + path "versions.yml", emit: versions + + +[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Found 5 outputs in modules/local/clairsto/main.nf +[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Outputs: {'indel_vcf': [[{'meta': {}}, {'indel.vcf.gz': {}}]], 'indel_tbi': [[{'meta': {}}, {'indel.vcf.gz.tbi': {}}]], 'snv_vcf': [[{'meta': {}}, {'snv.vcf.gz': {}}]], 'snv_tbi': [[{'meta': {}}, {'snv.vcf.gz.tbi': {}}]], 'versions': [{'versions.yml': {}}]} +[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Output data: + tuple val(meta), path("indel.vcf.gz"), emit: indel_vcf + tuple val(meta), path("indel.vcf.gz.tbi"), emit: indel_tbi + tuple val(meta), path("snv.vcf.gz"), emit: snv_vcf + tuple val(meta), path("snv.vcf.gz.tbi"), emit: snv_tbi + path "versions.yml", emit: versions + + +[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/local/clairsto/main.nf +[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Topics: {} +[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/local/fibertoolsrs/fire/main.nf +[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'bam': {}}]] +[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Found output_data: + // TODO nf-core: Named file extensions MUST be emitted for ALL output channels + tuple val(meta), path("*.bam"), emit: bam + // TODO nf-core: List additional required output channels/values here + path "versions.yml" , emit: versions + + +[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/local/fibertoolsrs/fire/main.nf +[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Outputs: {'bam': [[{'meta': {}}, {'*.bam': {}}]], 'versions': [{'versions.yml': {}}]} +[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Output data: + // TODO nf-core: Named file extensions MUST be emitted for ALL output channels + tuple val(meta), path("*.bam"), emit: bam + // TODO nf-core: List additional required output channels/values here + path "versions.yml" , emit: versions + + +[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/local/fibertoolsrs/fire/main.nf +[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Topics: {} +[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/local/fibertoolsrs/predictm6a/main.nf +[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'bam': {}}]] +[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Found output_data: + // TODO nf-core: Named file extensions MUST be emitted for ALL output channels + tuple val(meta), path("*.bam"), emit: bam + // TODO nf-core: List additional required output channels/values here + path "versions.yml" , emit: versions + + +[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/local/fibertoolsrs/predictm6a/main.nf +[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Outputs: {'bam': [[{'meta': {}}, {'*.bam': {}}]], 'versions': [{'versions.yml': {}}]} +[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Output data: + // TODO nf-core: Named file extensions MUST be emitted for ALL output channels + tuple val(meta), path("*.bam"), emit: bam + // TODO nf-core: List additional required output channels/values here + path "versions.yml" , emit: versions + + +[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/local/fibertoolsrs/predictm6a/main.nf +[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Topics: {} +[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/local/fibertoolsrs/qc/main.nf +[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'bam': {}}]] +[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Found output_data: + // TODO nf-core: Named file extensions MUST be emitted for ALL output channels + tuple val(meta), path("*.txt"), emit: qc_txt + // TODO nf-core: List additional required output channels/values here + path "versions.yml" , emit: versions + + +[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/local/fibertoolsrs/qc/main.nf +[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Outputs: {'qc_txt': [[{'meta': {}}, {'*.txt': {}}]], 'versions': [{'versions.yml': {}}]} +[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Output data: + // TODO nf-core: Named file extensions MUST be emitted for ALL output channels + tuple val(meta), path("*.txt"), emit: qc_txt + // TODO nf-core: List additional required output channels/values here + path "versions.yml" , emit: versions + + +[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/local/fibertoolsrs/qc/main.nf +[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Topics: {} +[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/local/fibertoolsrs/nucleosomes/main.nf +[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'bam': {}}]] +[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Found output_data: + // TODO nf-core: Named file extensions MUST be emitted for ALL output channels + tuple val(meta), path("*.bam"), emit: bam + // TODO nf-core: List additional required output channels/values here + path "versions.yml" , emit: versions + + +[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/local/fibertoolsrs/nucleosomes/main.nf +[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Outputs: {'bam': [[{'meta': {}}, {'*.bam': {}}]], 'versions': [{'versions.yml': {}}]} +[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Output data: + // TODO nf-core: Named file extensions MUST be emitted for ALL output channels + tuple val(meta), path("*.bam"), emit: bam + // TODO nf-core: List additional required output channels/values here + path "versions.yml" , emit: versions + + +[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/local/fibertoolsrs/nucleosomes/main.nf +[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Topics: {} +[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/local/vcfsplit/main.nf +[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'snv_vcf': {}}, {'indel_vcf': {}}]] +[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Found output_data: + tuple val(meta), path("*somatic.vcf.gz") , emit: somatic_vcf + tuple val(meta), path("*somatic.vcf.gz.tbi") , emit: somatic_tbi + tuple val(meta), path("*germline.vcf.gz") , emit: germline_vcf + tuple val(meta), path("*germline.vcf.gz.tbi") , emit: germline_tbi + + path "versions.yml" , emit: versions + + +[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Found 5 outputs in modules/local/vcfsplit/main.nf +[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Outputs: {'somatic_vcf': [[{'meta': {}}, {'*somatic.vcf.gz': {}}]], 'somatic_tbi': [[{'meta': {}}, {'*somatic.vcf.gz.tbi': {}}]], 'germline_vcf': [[{'meta': {}}, {'*germline.vcf.gz': {}}]], 'germline_tbi': [[{'meta': {}}, {'*germline.vcf.gz.tbi': {}}]], 'versions': [{'versions.yml': {}}]} +[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Output data: + tuple val(meta), path("*somatic.vcf.gz") , emit: somatic_vcf + tuple val(meta), path("*somatic.vcf.gz.tbi") , emit: somatic_tbi + tuple val(meta), path("*germline.vcf.gz") , emit: germline_vcf + tuple val(meta), path("*germline.vcf.gz.tbi") , emit: germline_tbi + + path "versions.yml" , emit: versions + + +[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/local/vcfsplit/main.nf +[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Topics: {} +[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Found 3 inputs in modules/local/clair3/main.nf +[2025-11-27 15:50:36,571] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'bam': {}}, {'bai': {}}, {'model': {}}, {'platform': {}}], [{'meta2': {}}, {'reference': {}}], [{'meta3': {}}, {'index': {}}]] +[2025-11-27 15:50:36,571] nf_core.components.nfcore_component [DEBUG ] Found output_data: + tuple val(meta), path("*merge_output.vcf.gz"), emit: vcf + tuple val(meta), path("*merge_output.vcf.gz.tbi"), emit: tbi + tuple val(meta), path("*phased_merge_output.vcf.gz"), emit: phased_vcf, optional: true + tuple val(meta), path("*phased_merge_output.vcf.gz.tbi"), emit: phased_tbi, optional: true + path "versions.yml", emit: versions + + +[2025-11-27 15:50:36,571] nf_core.components.nfcore_component [DEBUG ] Found 5 outputs in modules/local/clair3/main.nf +[2025-11-27 15:50:36,571] nf_core.components.nfcore_component [DEBUG ] Outputs: {'vcf': [[{'meta': {}}, {'*merge_output.vcf.gz': {}}]], 'tbi': [[{'meta': {}}, {'*merge_output.vcf.gz.tbi': {}}]], 'phased_vcf': [[{'meta': {}}, {'*phased_merge_output.vcf.gz': {}}]], 'phased_tbi': [[{'meta': {}}, {'*phased_merge_output.vcf.gz.tbi': {}}]], 'versions': [{'versions.yml': {}}]} +[2025-11-27 15:50:36,571] nf_core.components.nfcore_component [DEBUG ] Output data: + tuple val(meta), path("*merge_output.vcf.gz"), emit: vcf + tuple val(meta), path("*merge_output.vcf.gz.tbi"), emit: tbi + tuple val(meta), path("*phased_merge_output.vcf.gz"), emit: phased_vcf, optional: true + tuple val(meta), path("*phased_merge_output.vcf.gz.tbi"), emit: phased_tbi, optional: true + path "versions.yml", emit: versions + + +[2025-11-27 15:50:36,571] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/local/clair3/main.nf +[2025-11-27 15:50:36,571] nf_core.components.nfcore_component [DEBUG ] Topics: {} +[2025-11-27 15:50:36,573] nf_core.components.nfcore_component [DEBUG ] Found 8 inputs in modules/nf-core/ascat/main.nf +[2025-11-27 15:50:36,573] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'input_normal': {}}, {'index_normal': {}}, {'input_tumor': {}}, {'index_tumor': {}}], {'genomeVersion': {}}, {'allele_files': {}}, {'loci_files': {}}, {'bed_file': {}}, {'fasta': {}}, {'gc_file': {}}, {'rt_file': {}}] +[2025-11-27 15:50:36,573] nf_core.components.nfcore_component [DEBUG ] Found output_data: + tuple val(meta), path("*alleleFrequencies_chr*.txt"), emit: allelefreqs + tuple val(meta), path("*BAF.txt"), emit: bafs + tuple val(meta), path("*cnvs.txt"), emit: cnvs + tuple val(meta), path("*LogR.txt"), emit: logrs + tuple val(meta), path("*metrics.txt"), emit: metrics + tuple val(meta), path("*png"), emit: png + tuple val(meta), path("*pdf"), emit: pdf, optional: true + tuple val(meta), path("*purityploidy.txt"), emit: purityploidy + tuple val(meta), path("*segments.txt"), emit: segments + tuple val(meta), path("*segments_raw.txt"), emit: segments_raw, optional: true + path "versions.yml", emit: versions + + +[2025-11-27 15:50:36,573] nf_core.components.nfcore_component [DEBUG ] Found 11 outputs in modules/nf-core/ascat/main.nf +[2025-11-27 15:50:36,573] nf_core.components.nfcore_component [DEBUG ] Outputs: {'allelefreqs': [[{'meta': {}}, {'*alleleFrequencies_chr*.txt': {}}]], 'bafs': [[{'meta': {}}, {'*BAF.txt': {}}]], 'cnvs': [[{'meta': {}}, {'*cnvs.txt': {}}]], 'logrs': [[{'meta': {}}, {'*LogR.txt': {}}]], 'metrics': [[{'meta': {}}, {'*metrics.txt': {}}]], 'png': [[{'meta': {}}, {'*png': {}}]], 'pdf': [[{'meta': {}}, {'*pdf': {}}]], 'purityploidy': [[{'meta': {}}, {'*purityploidy.txt': {}}]], 'segments': [[{'meta': {}}, {'*segments.txt': {}}]], 'segments_raw': [[{'meta': {}}, {'*segments_raw.txt': {}}]], 'versions': [{'versions.yml': {}}]} +[2025-11-27 15:50:36,573] nf_core.components.nfcore_component [DEBUG ] Output data: + tuple val(meta), path("*alleleFrequencies_chr*.txt"), emit: allelefreqs + tuple val(meta), path("*BAF.txt"), emit: bafs + tuple val(meta), path("*cnvs.txt"), emit: cnvs + tuple val(meta), path("*LogR.txt"), emit: logrs + tuple val(meta), path("*metrics.txt"), emit: metrics + tuple val(meta), path("*png"), emit: png + tuple val(meta), path("*pdf"), emit: pdf, optional: true + tuple val(meta), path("*purityploidy.txt"), emit: purityploidy + tuple val(meta), path("*segments.txt"), emit: segments + tuple val(meta), path("*segments_raw.txt"), emit: segments_raw, optional: true + path "versions.yml", emit: versions + + +[2025-11-27 15:50:36,573] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/ascat/main.nf +[2025-11-27 15:50:36,573] nf_core.components.nfcore_component [DEBUG ] Topics: {} +[2025-11-27 15:50:36,574] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:50:36,575] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:50:36,839] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:50:36,851] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:50:36,851] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:50:36,852] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:50:36,852] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:50:36,884] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:50:36,887] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/ascat'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:50:36,888] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/ascat'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:50:36,986] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:50:37,056] nf_core.components.components_differ [DEBUG ] Applying patch to modules/nf-core/ascat/main.nf +[2025-11-27 15:50:37,056] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/nf-core/bcftools/concat/main.nf +[2025-11-27 15:50:37,057] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'vcfs': {}}, {'tbi': {}}]] +[2025-11-27 15:50:37,057] nf_core.components.nfcore_component [DEBUG ] Found output_data: + tuple val(meta), path("${prefix}.${extension}") , emit: vcf + tuple val(meta), path("${prefix}.${extension}.tbi"), emit: tbi, optional: true + tuple val(meta), path("${prefix}.${extension}.csi"), emit: csi, optional: true + path "versions.yml" , emit: versions + + +[2025-11-27 15:50:37,057] nf_core.components.nfcore_component [DEBUG ] Found 4 outputs in modules/nf-core/bcftools/concat/main.nf +[2025-11-27 15:50:37,057] nf_core.components.nfcore_component [DEBUG ] Outputs: {'vcf': [[{'meta': {}}, {'${prefix}.${extension}': {}}]], 'tbi': [[{'meta': {}}, {'${prefix}.${extension}.tbi': {}}]], 'csi': [[{'meta': {}}, {'${prefix}.${extension}.csi': {}}]], 'versions': [{'versions.yml': {}}]} +[2025-11-27 15:50:37,057] nf_core.components.nfcore_component [DEBUG ] Output data: + tuple val(meta), path("${prefix}.${extension}") , emit: vcf + tuple val(meta), path("${prefix}.${extension}.tbi"), emit: tbi, optional: true + tuple val(meta), path("${prefix}.${extension}.csi"), emit: csi, optional: true + path "versions.yml" , emit: versions + + +[2025-11-27 15:50:37,057] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/bcftools/concat/main.nf +[2025-11-27 15:50:37,057] nf_core.components.nfcore_component [DEBUG ] Topics: {} +[2025-11-27 15:50:37,057] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:50:37,058] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:50:37,092] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:50:37,103] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:50:37,103] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:50:37,103] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:50:37,104] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:50:37,135] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:50:37,138] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/bcftools/concat'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:50:37,139] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/bcftools/concat'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:50:37,225] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:50:37,309] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:50:37,310] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:50:37,343] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:50:37,353] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:50:37,354] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:50:37,354] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:50:37,354] git.cmd [DEBUG ] Popen(['git', 'checkout', 'e753770db613ce014b3c4bc94f6cba443427b726'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:50:38,018] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:50:38,212] nf_core.components.nfcore_component [DEBUG ] Found 4 inputs in modules/nf-core/bcftools/merge/main.nf +[2025-11-27 15:50:38,212] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'vcfs': {}}, {'tbis': {}}], [{'meta2': {}}, {'fasta': {}}], [{'meta3': {}}, {'fai': {}}], [{'meta4': {}}, {'bed': {}}]] +[2025-11-27 15:50:38,212] nf_core.components.nfcore_component [DEBUG ] Found output_data: + tuple val(meta), path("*.{bcf,vcf}{,.gz}"), emit: vcf + tuple val(meta), path("*.{csi,tbi}") , emit: index, optional: true + path "versions.yml" , emit: versions + + +[2025-11-27 15:50:38,212] nf_core.components.nfcore_component [DEBUG ] Found 3 outputs in modules/nf-core/bcftools/merge/main.nf +[2025-11-27 15:50:38,213] nf_core.components.nfcore_component [DEBUG ] Outputs: {'vcf': [[{'meta': {}}, {'*.{bcf,vcf}{,.gz}': {}}]], 'index': [[{'meta': {}}, {'*.{csi,tbi}': {}}]], 'versions': [{'versions.yml': {}}]} +[2025-11-27 15:50:38,213] nf_core.components.nfcore_component [DEBUG ] Output data: + tuple val(meta), path("*.{bcf,vcf}{,.gz}"), emit: vcf + tuple val(meta), path("*.{csi,tbi}") , emit: index, optional: true + path "versions.yml" , emit: versions + + +[2025-11-27 15:50:38,213] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/bcftools/merge/main.nf +[2025-11-27 15:50:38,213] nf_core.components.nfcore_component [DEBUG ] Topics: {} +[2025-11-27 15:50:38,213] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:50:38,213] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:50:38,275] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:50:38,286] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:50:38,287] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:50:38,287] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:50:38,288] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:50:38,346] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:50:38,350] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/bcftools/merge'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:50:38,351] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/bcftools/merge'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:50:38,436] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:50:38,518] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:50:38,518] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:50:38,566] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:50:38,578] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:50:38,578] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:50:38,578] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:50:38,579] git.cmd [DEBUG ] Popen(['git', 'checkout', 'f17049e03697726ace7499d2fe342f892594f6f3'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:50:42,382] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:50:45,573] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/nf-core/bcftools/sort/main.nf +[2025-11-27 15:50:45,573] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'vcf': {}}]] +[2025-11-27 15:50:45,573] nf_core.components.nfcore_component [DEBUG ] Found output_data: + tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf + tuple val(meta), path("*.tbi") , emit: tbi, optional: true + tuple val(meta), path("*.csi") , emit: csi, optional: true + path "versions.yml" , emit: versions + + +[2025-11-27 15:50:45,573] nf_core.components.nfcore_component [DEBUG ] Found 4 outputs in modules/nf-core/bcftools/sort/main.nf +[2025-11-27 15:50:45,573] nf_core.components.nfcore_component [DEBUG ] Outputs: {'vcf': [[{'meta': {}}, {'*.{vcf,vcf.gz,bcf,bcf.gz}': {}}]], 'tbi': [[{'meta': {}}, {'*.tbi': {}}]], 'csi': [[{'meta': {}}, {'*.csi': {}}]], 'versions': [{'versions.yml': {}}]} +[2025-11-27 15:50:45,573] nf_core.components.nfcore_component [DEBUG ] Output data: + tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf + tuple val(meta), path("*.tbi") , emit: tbi, optional: true + tuple val(meta), path("*.csi") , emit: csi, optional: true + path "versions.yml" , emit: versions + + +[2025-11-27 15:50:45,573] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/bcftools/sort/main.nf +[2025-11-27 15:50:45,573] nf_core.components.nfcore_component [DEBUG ] Topics: {} +[2025-11-27 15:50:45,573] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:50:45,574] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:50:45,713] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:50:45,727] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:50:45,727] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:50:45,727] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:50:45,728] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:50:45,865] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:50:45,868] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/bcftools/sort'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:50:45,869] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/bcftools/sort'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:50:45,959] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:50:46,043] nf_core.components.components_differ [DEBUG ] Applying patch to modules/nf-core/bcftools/sort/main.nf +[2025-11-27 15:50:46,044] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/nf-core/ensemblvep/download/main.nf +[2025-11-27 15:50:46,044] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'assembly': {}}, {'species': {}}, {'cache_version': {}}]] +[2025-11-27 15:50:46,044] nf_core.components.nfcore_component [DEBUG ] Found output_data: + tuple val(meta), path(prefix), emit: cache + path "versions.yml", emit: versions + + +[2025-11-27 15:50:46,044] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/nf-core/ensemblvep/download/main.nf +[2025-11-27 15:50:46,044] nf_core.components.nfcore_component [DEBUG ] Outputs: {'cache': [[{'meta': {}}, {'prefix': {}}]], 'versions': [{'versions.yml': {}}]} +[2025-11-27 15:50:46,044] nf_core.components.nfcore_component [DEBUG ] Output data: + tuple val(meta), path(prefix), emit: cache + path "versions.yml", emit: versions + + +[2025-11-27 15:50:46,044] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/ensemblvep/download/main.nf +[2025-11-27 15:50:46,044] nf_core.components.nfcore_component [DEBUG ] Topics: {} +[2025-11-27 15:50:46,044] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:50:46,045] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:50:46,151] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:50:46,164] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:50:46,164] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:50:46,164] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:50:46,165] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:50:46,208] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:50:46,212] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/ensemblvep/download'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:50:46,213] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/ensemblvep/download'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:50:46,324] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:50:46,402] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:50:46,402] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:50:46,455] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:50:46,467] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:50:46,467] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:50:46,467] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:50:46,468] git.cmd [DEBUG ] Popen(['git', 'checkout', '2fcc53751152a999bfc9c24f75f494b9e5bb338f'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:50:49,974] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:50:53,302] nf_core.components.nfcore_component [DEBUG ] Found 9 inputs in modules/nf-core/ensemblvep/vep/main.nf +[2025-11-27 15:50:53,302] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'vcf': {}}, {'custom_extra_files': {}}], {'genome': {}}, {'species': {}}, {'cache_version': {}}, {'cache': {}}, [{'meta2': {}}, {'fasta': {}}], {'extra_files': {}}, {'custom_vep': {}}, {'custom_vep_tbi': {}}] +[2025-11-27 15:50:53,302] nf_core.components.nfcore_component [DEBUG ] Found output_data: + tuple val(meta), path("*.vcf.gz"), emit: vcf, optional: true + tuple val(meta), path("*.vcf.gz.tbi"), emit: tbi, optional: true + tuple val(meta), path("*.tab.gz"), emit: tab, optional: true + tuple val(meta), path("*.json.gz"), emit: json, optional: true + path "*.html", emit: report, optional: true + path "versions.yml", emit: versions + + +[2025-11-27 15:50:53,302] nf_core.components.nfcore_component [DEBUG ] Found 6 outputs in modules/nf-core/ensemblvep/vep/main.nf +[2025-11-27 15:50:53,302] nf_core.components.nfcore_component [DEBUG ] Outputs: {'vcf': [[{'meta': {}}, {'*.vcf.gz': {}}]], 'tbi': [[{'meta': {}}, {'*.vcf.gz.tbi': {}}]], 'tab': [[{'meta': {}}, {'*.tab.gz': {}}]], 'json': [[{'meta': {}}, {'*.json.gz': {}}]], 'report': [{'*.html': {}}], 'versions': [{'versions.yml': {}}]} +[2025-11-27 15:50:53,302] nf_core.components.nfcore_component [DEBUG ] Output data: + tuple val(meta), path("*.vcf.gz"), emit: vcf, optional: true + tuple val(meta), path("*.vcf.gz.tbi"), emit: tbi, optional: true + tuple val(meta), path("*.tab.gz"), emit: tab, optional: true + tuple val(meta), path("*.json.gz"), emit: json, optional: true + path "*.html", emit: report, optional: true + path "versions.yml", emit: versions + + +[2025-11-27 15:50:53,302] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/ensemblvep/vep/main.nf +[2025-11-27 15:50:53,302] nf_core.components.nfcore_component [DEBUG ] Topics: {} +[2025-11-27 15:50:53,302] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:50:53,303] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:50:53,408] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:50:53,420] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:50:53,420] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:50:53,420] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:50:53,421] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:50:53,518] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:50:53,522] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/ensemblvep/vep'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:50:53,523] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/ensemblvep/vep'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:50:53,631] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:50:53,709] nf_core.components.components_differ [DEBUG ] Applying patch to modules/nf-core/ensemblvep/vep/main.nf +[2025-11-27 15:50:53,709] nf_core.components.nfcore_component [DEBUG ] Found 3 inputs in modules/nf-core/longphase/haplotag/main.nf +[2025-11-27 15:50:53,709] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'bam': {}}, {'bai': {}}, {'snps': {}}, {'svs': {}}, {'mods': {}}], [{'meta2': {}}, {'fasta': {}}], [{'meta3': {}}, {'fai': {}}]] +[2025-11-27 15:50:53,710] nf_core.components.nfcore_component [DEBUG ] Found output_data: + tuple val(meta), path("*.{bam,cram}"), emit: bam + tuple val(meta), path("*.log") , emit: log , optional: true + path "versions.yml" , emit: versions + + +[2025-11-27 15:50:53,710] nf_core.components.nfcore_component [DEBUG ] Found 3 outputs in modules/nf-core/longphase/haplotag/main.nf +[2025-11-27 15:50:53,710] nf_core.components.nfcore_component [DEBUG ] Outputs: {'bam': [[{'meta': {}}, {'*.{bam,cram}': {}}]], 'log': [[{'meta': {}}, {'*.log': {}}]], 'versions': [{'versions.yml': {}}]} +[2025-11-27 15:50:53,710] nf_core.components.nfcore_component [DEBUG ] Output data: + tuple val(meta), path("*.{bam,cram}"), emit: bam + tuple val(meta), path("*.log") , emit: log , optional: true + path "versions.yml" , emit: versions + + +[2025-11-27 15:50:53,710] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/longphase/haplotag/main.nf +[2025-11-27 15:50:53,710] nf_core.components.nfcore_component [DEBUG ] Topics: {} +[2025-11-27 15:50:53,710] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:50:53,711] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:50:53,792] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:50:53,804] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:50:53,805] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:50:53,806] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:50:53,806] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:50:53,874] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:50:53,878] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/longphase/haplotag'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:50:53,879] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/longphase/haplotag'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:50:53,991] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:50:54,094] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:50:54,095] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:50:54,185] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:50:54,199] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:50:54,199] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:50:54,200] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:50:54,200] git.cmd [DEBUG ] Popen(['git', 'checkout', '41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:50:58,312] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:02,039] nf_core.components.nfcore_component [DEBUG ] Found 3 inputs in modules/nf-core/longphase/phase/main.nf +[2025-11-27 15:51:02,039] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'bam': {}}, {'bai': {}}, {'snps': {}}, {'svs': {}}, {'mods': {}}], [{'meta2': {}}, {'fasta': {}}], [{'meta3': {}}, {'fai': {}}]] +[2025-11-27 15:51:02,039] nf_core.components.nfcore_component [DEBUG ] Found output_data: + tuple val(meta), path("*.vcf.gz") , emit: vcf + tuple val(meta), path("*.vcf.gz.tbi") , emit: tbi + path "versions.yml" , emit: versions + + +[2025-11-27 15:51:02,039] nf_core.components.nfcore_component [DEBUG ] Found 3 outputs in modules/nf-core/longphase/phase/main.nf +[2025-11-27 15:51:02,039] nf_core.components.nfcore_component [DEBUG ] Outputs: {'vcf': [[{'meta': {}}, {'*.vcf.gz': {}}]], 'tbi': [[{'meta': {}}, {'*.vcf.gz.tbi': {}}]], 'versions': [{'versions.yml': {}}]} +[2025-11-27 15:51:02,039] nf_core.components.nfcore_component [DEBUG ] Output data: + tuple val(meta), path("*.vcf.gz") , emit: vcf + tuple val(meta), path("*.vcf.gz.tbi") , emit: tbi + path "versions.yml" , emit: versions + + +[2025-11-27 15:51:02,039] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/longphase/phase/main.nf +[2025-11-27 15:51:02,039] nf_core.components.nfcore_component [DEBUG ] Topics: {} +[2025-11-27 15:51:02,039] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:51:02,040] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:02,408] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:02,419] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:51:02,419] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:51:02,420] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:51:02,421] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:02,475] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:51:02,478] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/longphase/phase'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:02,479] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/longphase/phase'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:02,590] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:51:02,695] nf_core.components.components_differ [DEBUG ] Applying patch to modules/nf-core/longphase/phase/main.nf +[2025-11-27 15:51:02,695] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:51:02,696] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:02,749] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:02,761] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:51:02,761] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:51:02,761] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:51:02,762] git.cmd [DEBUG ] Popen(['git', 'checkout', '41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:05,703] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:09,496] nf_core.components.nfcore_component [DEBUG ] Found 6 inputs in modules/nf-core/minimap2/align/main.nf +[2025-11-27 15:51:09,496] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'reads': {}}], [{'meta2': {}}, {'reference': {}}], {'bam_format': {}}, {'bam_index_extension': {}}, {'cigar_paf_format': {}}, {'cigar_bam': {}}] +[2025-11-27 15:51:09,496] nf_core.components.nfcore_component [DEBUG ] Found output_data: + tuple val(meta), path("*.paf") , optional: true, emit: paf + tuple val(meta), path("*.bam") , optional: true, emit: bam + tuple val(meta), path("*.bam.${bam_index_extension}"), optional: true, emit: index + path "versions.yml" , emit: versions + + +[2025-11-27 15:51:09,496] nf_core.components.nfcore_component [DEBUG ] Found 4 outputs in modules/nf-core/minimap2/align/main.nf +[2025-11-27 15:51:09,496] nf_core.components.nfcore_component [DEBUG ] Outputs: {'paf': [[{'meta': {}}, {'*.paf': {}}]], 'bam': [[{'meta': {}}, {'*.bam': {}}]], 'index': [[{'meta': {}}, {'*.bam.${bam_index_extension}': {}}]], 'versions': [{'versions.yml': {}}]} +[2025-11-27 15:51:09,496] nf_core.components.nfcore_component [DEBUG ] Output data: + tuple val(meta), path("*.paf") , optional: true, emit: paf + tuple val(meta), path("*.bam") , optional: true, emit: bam + tuple val(meta), path("*.bam.${bam_index_extension}"), optional: true, emit: index + path "versions.yml" , emit: versions + + +[2025-11-27 15:51:09,496] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/minimap2/align/main.nf +[2025-11-27 15:51:09,496] nf_core.components.nfcore_component [DEBUG ] Topics: {} +[2025-11-27 15:51:09,496] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:51:09,497] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:09,655] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:09,667] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:51:09,667] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:51:09,667] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:51:09,668] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:09,808] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:51:09,812] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/minimap2/align'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:09,813] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/minimap2/align'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:09,901] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:51:10,040] nf_core.components.components_differ [DEBUG ] Applying patch to modules/nf-core/minimap2/align/main.nf +[2025-11-27 15:51:10,041] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:51:10,041] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:10,141] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:10,153] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:51:10,153] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:51:10,154] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:51:10,154] git.cmd [DEBUG ] Popen(['git', 'checkout', '41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:13,177] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:16,904] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/nf-core/minimap2/index/main.nf +[2025-11-27 15:51:16,904] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'fasta': {}}]] +[2025-11-27 15:51:16,904] nf_core.components.nfcore_component [DEBUG ] Found output_data: + tuple val(meta), path("*.mmi"), emit: index + path "versions.yml" , emit: versions + + +[2025-11-27 15:51:16,904] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/nf-core/minimap2/index/main.nf +[2025-11-27 15:51:16,904] nf_core.components.nfcore_component [DEBUG ] Outputs: {'index': [[{'meta': {}}, {'*.mmi': {}}]], 'versions': [{'versions.yml': {}}]} +[2025-11-27 15:51:16,904] nf_core.components.nfcore_component [DEBUG ] Output data: + tuple val(meta), path("*.mmi"), emit: index + path "versions.yml" , emit: versions + + +[2025-11-27 15:51:16,904] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/minimap2/index/main.nf +[2025-11-27 15:51:16,904] nf_core.components.nfcore_component [DEBUG ] Topics: {} +[2025-11-27 15:51:16,904] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:51:16,905] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:17,209] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:17,221] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:51:17,221] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:51:17,222] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:51:17,222] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:17,280] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:51:17,284] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/minimap2/index'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:17,285] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/minimap2/index'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:17,372] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:51:17,510] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:51:17,510] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:17,570] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:17,582] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:51:17,583] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:51:17,583] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:51:17,583] git.cmd [DEBUG ] Popen(['git', 'checkout', '41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:20,761] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:24,622] nf_core.components.nfcore_component [DEBUG ] Found 3 inputs in modules/nf-core/modkit/pileup/main.nf +[2025-11-27 15:51:24,623] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'bam': {}}, {'bai': {}}], [{'meta2': {}}, {'fasta': {}}, {'fai': {}}], [{'meta3': {}}, {'bed': {}}]] +[2025-11-27 15:51:24,623] nf_core.components.nfcore_component [DEBUG ] Found output_data: + tuple val(meta), path("*.bed") , emit: bed , optional: true + tuple val(meta), path("*.bedgraph"), emit: bedgraph, optional: true + tuple val(meta), path("*.log") , emit: log , optional: true + path "versions.yml" , emit: versions + + +[2025-11-27 15:51:24,623] nf_core.components.nfcore_component [DEBUG ] Found 4 outputs in modules/nf-core/modkit/pileup/main.nf +[2025-11-27 15:51:24,623] nf_core.components.nfcore_component [DEBUG ] Outputs: {'bed': [[{'meta': {}}, {'*.bed': {}}]], 'bedgraph': [[{'meta': {}}, {'*.bedgraph': {}}]], 'log': [[{'meta': {}}, {'*.log': {}}]], 'versions': [{'versions.yml': {}}]} +[2025-11-27 15:51:24,623] nf_core.components.nfcore_component [DEBUG ] Output data: + tuple val(meta), path("*.bed") , emit: bed , optional: true + tuple val(meta), path("*.bedgraph"), emit: bedgraph, optional: true + tuple val(meta), path("*.log") , emit: log , optional: true + path "versions.yml" , emit: versions + + +[2025-11-27 15:51:24,623] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/modkit/pileup/main.nf +[2025-11-27 15:51:24,623] nf_core.components.nfcore_component [DEBUG ] Topics: {} +[2025-11-27 15:51:24,623] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:51:24,624] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:24,815] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:24,826] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:51:24,827] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:51:24,827] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:51:24,828] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:24,997] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:51:25,000] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/modkit/pileup'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:25,002] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/modkit/pileup'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:25,119] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:51:25,234] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:51:25,235] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:25,374] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:25,386] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:51:25,386] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:51:25,386] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:51:25,387] git.cmd [DEBUG ] Popen(['git', 'checkout', '41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:28,381] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:32,189] nf_core.components.nfcore_component [DEBUG ] Found 2 inputs in modules/nf-core/mosdepth/main.nf +[2025-11-27 15:51:32,189] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'bam': {}}, {'bai': {}}, {'bed': {}}], [{'meta2': {}}, {'fasta': {}}]] +[2025-11-27 15:51:32,189] nf_core.components.nfcore_component [DEBUG ] Found output_data: + tuple val(meta), path('*.global.dist.txt') , emit: global_txt + tuple val(meta), path('*.summary.txt') , emit: summary_txt + tuple val(meta), path('*.region.dist.txt') , optional:true, emit: regions_txt + tuple val(meta), path('*.per-base.d4') , optional:true, emit: per_base_d4 + tuple val(meta), path('*.per-base.bed.gz') , optional:true, emit: per_base_bed + tuple val(meta), path('*.per-base.bed.gz.csi') , optional:true, emit: per_base_csi + tuple val(meta), path('*.regions.bed.gz') , optional:true, emit: regions_bed + tuple val(meta), path('*.regions.bed.gz.csi') , optional:true, emit: regions_csi + tuple val(meta), path('*.quantized.bed.gz') , optional:true, emit: quantized_bed + tuple val(meta), path('*.quantized.bed.gz.csi') , optional:true, emit: quantized_csi + tuple val(meta), path('*.thresholds.bed.gz') , optional:true, emit: thresholds_bed + tuple val(meta), path('*.thresholds.bed.gz.csi'), optional:true, emit: thresholds_csi + path "versions.yml" , emit: versions + + +[2025-11-27 15:51:32,190] nf_core.components.nfcore_component [DEBUG ] Found 13 outputs in modules/nf-core/mosdepth/main.nf +[2025-11-27 15:51:32,190] nf_core.components.nfcore_component [DEBUG ] Outputs: {'global_txt': [[{'meta': {}}, {'*.global.dist.txt': {}}]], 'summary_txt': [[{'meta': {}}, {'*.summary.txt': {}}]], 'regions_txt': [[{'meta': {}}, {'*.region.dist.txt': {}}]], 'per_base_d4': [[{'meta': {}}, {'*.per-base.d4': {}}]], 'per_base_bed': [[{'meta': {}}, {'*.per-base.bed.gz': {}}]], 'per_base_csi': [[{'meta': {}}, {'*.per-base.bed.gz.csi': {}}]], 'regions_bed': [[{'meta': {}}, {'*.regions.bed.gz': {}}]], 'regions_csi': [[{'meta': {}}, {'*.regions.bed.gz.csi': {}}]], 'quantized_bed': [[{'meta': {}}, {'*.quantized.bed.gz': {}}]], 'quantized_csi': [[{'meta': {}}, {'*.quantized.bed.gz.csi': {}}]], 'thresholds_bed': [[{'meta': {}}, {'*.thresholds.bed.gz': {}}]], 'thresholds_csi': [[{'meta': {}}, {'*.thresholds.bed.gz.csi': {}}]], 'versions': [{'versions.yml': {}}]} +[2025-11-27 15:51:32,190] nf_core.components.nfcore_component [DEBUG ] Output data: + tuple val(meta), path('*.global.dist.txt') , emit: global_txt + tuple val(meta), path('*.summary.txt') , emit: summary_txt + tuple val(meta), path('*.region.dist.txt') , optional:true, emit: regions_txt + tuple val(meta), path('*.per-base.d4') , optional:true, emit: per_base_d4 + tuple val(meta), path('*.per-base.bed.gz') , optional:true, emit: per_base_bed + tuple val(meta), path('*.per-base.bed.gz.csi') , optional:true, emit: per_base_csi + tuple val(meta), path('*.regions.bed.gz') , optional:true, emit: regions_bed + tuple val(meta), path('*.regions.bed.gz.csi') , optional:true, emit: regions_csi + tuple val(meta), path('*.quantized.bed.gz') , optional:true, emit: quantized_bed + tuple val(meta), path('*.quantized.bed.gz.csi') , optional:true, emit: quantized_csi + tuple val(meta), path('*.thresholds.bed.gz') , optional:true, emit: thresholds_bed + tuple val(meta), path('*.thresholds.bed.gz.csi'), optional:true, emit: thresholds_csi + path "versions.yml" , emit: versions + + +[2025-11-27 15:51:32,190] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/mosdepth/main.nf +[2025-11-27 15:51:32,190] nf_core.components.nfcore_component [DEBUG ] Topics: {} +[2025-11-27 15:51:32,190] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:51:32,191] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:32,284] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:32,295] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:51:32,296] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:51:32,297] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:51:32,298] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:32,363] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:51:32,367] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/mosdepth'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:32,368] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/mosdepth'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:32,456] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:51:32,599] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:51:32,600] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:32,663] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:32,674] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:51:32,675] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:51:32,675] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:51:32,675] git.cmd [DEBUG ] Popen(['git', 'checkout', '41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:35,682] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:39,445] nf_core.components.nfcore_component [DEBUG ] Found 6 inputs in modules/nf-core/multiqc/main.nf +[2025-11-27 15:51:39,445] nf_core.components.nfcore_component [DEBUG ] Inputs: [{'multiqc_files': {}}, {'multiqc_config': {}}, {'extra_multiqc_config': {}}, {'multiqc_logo': {}}, {'replace_names': {}}, {'sample_names': {}}] +[2025-11-27 15:51:39,445] nf_core.components.nfcore_component [DEBUG ] Found output_data: + path "*multiqc_report.html", emit: report + path "*_data" , emit: data + path "*_plots" , optional:true, emit: plots + path "versions.yml" , emit: versions + + +[2025-11-27 15:51:39,445] nf_core.components.nfcore_component [DEBUG ] Found 4 outputs in modules/nf-core/multiqc/main.nf +[2025-11-27 15:51:39,445] nf_core.components.nfcore_component [DEBUG ] Outputs: {'report': [{'*multiqc_report.html': {}}], 'data': [{'*_data': {}}], 'plots': [{'*_plots': {}}], 'versions': [{'versions.yml': {}}]} +[2025-11-27 15:51:39,445] nf_core.components.nfcore_component [DEBUG ] Output data: + path "*multiqc_report.html", emit: report + path "*_data" , emit: data + path "*_plots" , optional:true, emit: plots + path "versions.yml" , emit: versions + + +[2025-11-27 15:51:39,445] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/multiqc/main.nf +[2025-11-27 15:51:39,445] nf_core.components.nfcore_component [DEBUG ] Topics: {} +[2025-11-27 15:51:39,445] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:51:39,446] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:39,663] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:39,675] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:51:39,675] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:51:39,676] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:51:39,677] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:39,806] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:51:39,810] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/multiqc'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:39,811] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/multiqc'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:39,903] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:51:40,049] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:51:40,050] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:40,147] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:40,160] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:51:40,160] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:51:40,161] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:51:40,161] git.cmd [DEBUG ] Popen(['git', 'checkout', 'a4488d3d09244f29fb4606ba4eef85d59dcc6ad8'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:43,079] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:46,118] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/nf-core/pigz/uncompress/main.nf +[2025-11-27 15:51:46,119] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'zip': {}}]] +[2025-11-27 15:51:46,119] nf_core.components.nfcore_component [DEBUG ] Found output_data: + tuple val(meta), path("${uncompressed_filename}") , emit: file + path "versions.yml" , emit: versions + + +[2025-11-27 15:51:46,119] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/nf-core/pigz/uncompress/main.nf +[2025-11-27 15:51:46,119] nf_core.components.nfcore_component [DEBUG ] Outputs: {'file': [[{'meta': {}}, {'${uncompressed_filename}': {}}]], 'versions': [{'versions.yml': {}}]} +[2025-11-27 15:51:46,119] nf_core.components.nfcore_component [DEBUG ] Output data: + tuple val(meta), path("${uncompressed_filename}") , emit: file + path "versions.yml" , emit: versions + + +[2025-11-27 15:51:46,119] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/pigz/uncompress/main.nf +[2025-11-27 15:51:46,119] nf_core.components.nfcore_component [DEBUG ] Topics: {} +[2025-11-27 15:51:46,119] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:51:46,120] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:46,170] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:46,183] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:51:46,184] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:51:46,184] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:51:46,185] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:46,235] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:51:46,239] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/pigz/uncompress'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:46,240] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/pigz/uncompress'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:46,362] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:51:46,485] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:51:46,486] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:46,557] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:46,569] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:51:46,569] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:51:46,569] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:51:46,570] git.cmd [DEBUG ] Popen(['git', 'checkout', '41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:49,638] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:53,446] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/nf-core/samtools/cat/main.nf +[2025-11-27 15:51:53,446] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'input_files': {}}]] +[2025-11-27 15:51:53,446] nf_core.components.nfcore_component [DEBUG ] Found output_data: + tuple val(meta), path("${prefix}.bam") , optional:true, emit: bam + tuple val(meta), path("${prefix}.cram"), optional:true, emit: cram + path "versions.yml" , emit: versions + + + +[2025-11-27 15:51:53,446] nf_core.components.nfcore_component [DEBUG ] Found 3 outputs in modules/nf-core/samtools/cat/main.nf +[2025-11-27 15:51:53,446] nf_core.components.nfcore_component [DEBUG ] Outputs: {'bam': [[{'meta': {}}, {'${prefix}.bam': {}}]], 'cram': [[{'meta': {}}, {'${prefix}.cram': {}}]], 'versions': [{'versions.yml': {}}]} +[2025-11-27 15:51:53,446] nf_core.components.nfcore_component [DEBUG ] Output data: + tuple val(meta), path("${prefix}.bam") , optional:true, emit: bam + tuple val(meta), path("${prefix}.cram"), optional:true, emit: cram + path "versions.yml" , emit: versions + + + +[2025-11-27 15:51:53,446] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/samtools/cat/main.nf +[2025-11-27 15:51:53,446] nf_core.components.nfcore_component [DEBUG ] Topics: {} +[2025-11-27 15:51:53,446] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:51:53,447] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:53,665] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:53,676] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:51:53,676] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:51:53,677] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:51:53,678] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:53,816] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:51:53,820] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/samtools/cat'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:53,821] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/samtools/cat'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:53,937] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:51:54,075] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:51:54,076] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:54,183] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:54,194] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:51:54,195] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:51:54,195] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:51:54,195] git.cmd [DEBUG ] Popen(['git', 'checkout', '41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:51:57,097] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:00,645] nf_core.components.nfcore_component [DEBUG ] Found 3 inputs in modules/nf-core/samtools/faidx/main.nf +[2025-11-27 15:52:00,645] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'fasta': {}}], [{'meta2': {}}, {'fai': {}}], {'get_sizes': {}}] +[2025-11-27 15:52:00,645] nf_core.components.nfcore_component [DEBUG ] Found output_data: + tuple val(meta), path ("*.{fa,fasta}") , emit: fa, optional: true + tuple val(meta), path ("*.sizes") , emit: sizes, optional: true + tuple val(meta), path ("*.fai") , emit: fai, optional: true + tuple val(meta), path ("*.gzi") , emit: gzi, optional: true + path "versions.yml" , emit: versions + + +[2025-11-27 15:52:00,645] nf_core.components.nfcore_component [DEBUG ] Found 5 outputs in modules/nf-core/samtools/faidx/main.nf +[2025-11-27 15:52:00,645] nf_core.components.nfcore_component [DEBUG ] Outputs: {'fa': [[{'meta': {}}, {'*.{fa,fasta}': {}}]], 'sizes': [[{'meta': {}}, {'*.sizes': {}}]], 'fai': [[{'meta': {}}, {'*.fai': {}}]], 'gzi': [[{'meta': {}}, {'*.gzi': {}}]], 'versions': [{'versions.yml': {}}]} +[2025-11-27 15:52:00,645] nf_core.components.nfcore_component [DEBUG ] Output data: + tuple val(meta), path ("*.{fa,fasta}") , emit: fa, optional: true + tuple val(meta), path ("*.sizes") , emit: sizes, optional: true + tuple val(meta), path ("*.fai") , emit: fai, optional: true + tuple val(meta), path ("*.gzi") , emit: gzi, optional: true + path "versions.yml" , emit: versions + + +[2025-11-27 15:52:00,645] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/samtools/faidx/main.nf +[2025-11-27 15:52:00,645] nf_core.components.nfcore_component [DEBUG ] Topics: {} +[2025-11-27 15:52:00,645] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:52:00,646] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:00,838] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:00,851] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:52:00,851] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:52:00,851] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:52:00,852] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:01,041] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:52:01,045] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/samtools/faidx'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:01,046] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/samtools/faidx'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:01,137] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:52:01,305] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:52:01,306] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:01,372] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:01,385] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:52:01,385] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:52:01,386] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:52:01,386] git.cmd [DEBUG ] Popen(['git', 'checkout', '41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:04,805] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:08,779] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/nf-core/samtools/flagstat/main.nf +[2025-11-27 15:52:08,779] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'bam': {}}, {'bai': {}}]] +[2025-11-27 15:52:08,779] nf_core.components.nfcore_component [DEBUG ] Found output_data: + tuple val(meta), path("*.flagstat"), emit: flagstat + path "versions.yml" , emit: versions + + +[2025-11-27 15:52:08,779] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/nf-core/samtools/flagstat/main.nf +[2025-11-27 15:52:08,779] nf_core.components.nfcore_component [DEBUG ] Outputs: {'flagstat': [[{'meta': {}}, {'*.flagstat': {}}]], 'versions': [{'versions.yml': {}}]} +[2025-11-27 15:52:08,779] nf_core.components.nfcore_component [DEBUG ] Output data: + tuple val(meta), path("*.flagstat"), emit: flagstat + path "versions.yml" , emit: versions + + +[2025-11-27 15:52:08,779] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/samtools/flagstat/main.nf +[2025-11-27 15:52:08,779] nf_core.components.nfcore_component [DEBUG ] Topics: {} +[2025-11-27 15:52:08,779] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:52:08,780] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:09,027] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:09,038] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:52:09,038] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:52:09,039] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:52:09,040] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:09,096] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:52:09,100] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/samtools/flagstat'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:09,101] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/samtools/flagstat'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:09,188] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:52:09,355] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:52:09,356] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:09,413] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:09,426] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:52:09,426] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:52:09,426] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:52:09,426] git.cmd [DEBUG ] Popen(['git', 'checkout', '41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:12,547] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:16,622] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/nf-core/samtools/idxstats/main.nf +[2025-11-27 15:52:16,622] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'bam': {}}, {'bai': {}}]] +[2025-11-27 15:52:16,622] nf_core.components.nfcore_component [DEBUG ] Found output_data: + tuple val(meta), path("*.idxstats"), emit: idxstats + path "versions.yml" , emit: versions + + +[2025-11-27 15:52:16,623] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/nf-core/samtools/idxstats/main.nf +[2025-11-27 15:52:16,623] nf_core.components.nfcore_component [DEBUG ] Outputs: {'idxstats': [[{'meta': {}}, {'*.idxstats': {}}]], 'versions': [{'versions.yml': {}}]} +[2025-11-27 15:52:16,623] nf_core.components.nfcore_component [DEBUG ] Output data: + tuple val(meta), path("*.idxstats"), emit: idxstats + path "versions.yml" , emit: versions + + +[2025-11-27 15:52:16,623] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/samtools/idxstats/main.nf +[2025-11-27 15:52:16,623] nf_core.components.nfcore_component [DEBUG ] Topics: {} +[2025-11-27 15:52:16,623] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:52:16,623] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:16,766] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:16,778] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:52:16,778] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:52:16,779] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:52:16,779] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:16,892] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:52:16,896] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/samtools/idxstats'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:16,897] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/samtools/idxstats'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:16,985] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:52:17,153] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:52:17,154] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:17,256] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:17,268] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:52:17,268] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:52:17,269] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:52:17,269] git.cmd [DEBUG ] Popen(['git', 'checkout', '41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:20,320] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:23,973] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/nf-core/samtools/index/main.nf +[2025-11-27 15:52:23,973] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'input': {}}]] +[2025-11-27 15:52:23,973] nf_core.components.nfcore_component [DEBUG ] Found output_data: + tuple val(meta), path("*.bai") , optional:true, emit: bai + tuple val(meta), path("*.csi") , optional:true, emit: csi + tuple val(meta), path("*.crai"), optional:true, emit: crai + path "versions.yml" , emit: versions + + +[2025-11-27 15:52:23,973] nf_core.components.nfcore_component [DEBUG ] Found 4 outputs in modules/nf-core/samtools/index/main.nf +[2025-11-27 15:52:23,973] nf_core.components.nfcore_component [DEBUG ] Outputs: {'bai': [[{'meta': {}}, {'*.bai': {}}]], 'csi': [[{'meta': {}}, {'*.csi': {}}]], 'crai': [[{'meta': {}}, {'*.crai': {}}]], 'versions': [{'versions.yml': {}}]} +[2025-11-27 15:52:23,973] nf_core.components.nfcore_component [DEBUG ] Output data: + tuple val(meta), path("*.bai") , optional:true, emit: bai + tuple val(meta), path("*.csi") , optional:true, emit: csi + tuple val(meta), path("*.crai"), optional:true, emit: crai + path "versions.yml" , emit: versions + + +[2025-11-27 15:52:23,974] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/samtools/index/main.nf +[2025-11-27 15:52:23,974] nf_core.components.nfcore_component [DEBUG ] Topics: {} +[2025-11-27 15:52:23,974] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:52:23,974] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:24,244] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:24,256] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:52:24,256] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:52:24,257] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:52:24,257] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:24,308] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:52:24,312] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/samtools/index'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:24,313] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/samtools/index'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:24,401] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:52:24,568] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:52:24,569] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:24,620] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:24,631] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:52:24,632] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:52:24,632] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:52:24,632] git.cmd [DEBUG ] Popen(['git', 'checkout', '41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:27,563] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:31,361] nf_core.components.nfcore_component [DEBUG ] Found 2 inputs in modules/nf-core/samtools/stats/main.nf +[2025-11-27 15:52:31,361] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'input': {}}, {'input_index': {}}], [{'meta2': {}}, {'fasta': {}}]] +[2025-11-27 15:52:31,361] nf_core.components.nfcore_component [DEBUG ] Found output_data: + tuple val(meta), path("*.stats"), emit: stats + path "versions.yml" , emit: versions + + +[2025-11-27 15:52:31,361] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/nf-core/samtools/stats/main.nf +[2025-11-27 15:52:31,361] nf_core.components.nfcore_component [DEBUG ] Outputs: {'stats': [[{'meta': {}}, {'*.stats': {}}]], 'versions': [{'versions.yml': {}}]} +[2025-11-27 15:52:31,361] nf_core.components.nfcore_component [DEBUG ] Output data: + tuple val(meta), path("*.stats"), emit: stats + path "versions.yml" , emit: versions + + +[2025-11-27 15:52:31,361] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/samtools/stats/main.nf +[2025-11-27 15:52:31,361] nf_core.components.nfcore_component [DEBUG ] Topics: {} +[2025-11-27 15:52:31,361] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:52:31,362] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:31,494] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:31,506] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:52:31,507] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:52:31,507] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:52:31,508] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:31,610] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:52:31,614] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/samtools/stats'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:31,615] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/samtools/stats'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:31,702] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:52:31,878] nf_core.components.components_differ [DEBUG ] Applying patch to modules/nf-core/samtools/stats/main.nf +[2025-11-27 15:52:31,878] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:52:31,879] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:31,963] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:31,975] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:52:31,976] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:52:31,976] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:52:31,976] git.cmd [DEBUG ] Popen(['git', 'checkout', '41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:34,930] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:38,673] nf_core.components.nfcore_component [DEBUG ] Found 2 inputs in modules/nf-core/severus/main.nf +[2025-11-27 15:52:38,673] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'target_input': {}}, {'target_index': {}}, {'control_input': {}}, {'control_index': {}}, {'vcf': {}}, {'tbi': {}}], [{'meta2': {}}, {'bed': {}}, {'pon_path': {}}]] +[2025-11-27 15:52:38,673] nf_core.components.nfcore_component [DEBUG ] Found output_data: + tuple val(meta), path("severus.log") , emit: log + tuple val(meta), path("read_qual.txt") , emit: read_qual + tuple val(meta), path("breakpoints_double.csv") , emit: breakpoints_double + tuple val(meta), path("read_alignments") , emit: read_alignments , optional: true + tuple val(meta), path("read_ids.csv") , emit: read_ids , optional: true + tuple val(meta), path("severus_collaped_dup.bed") , emit: collapsed_dup , optional: true + tuple val(meta), path("severus_LOH.bed") , emit: loh , optional: true + tuple val(meta), path("all_SVs/severus_all.vcf.gz") , emit: all_vcf , optional: true + tuple val(meta), path("all_SVs/severus_all.vcf.gz.tbi") , emit: all_tbi , optional: true + tuple val(meta), path("all_SVs/breakpoint_clusters_list.tsv") , emit: all_breakpoints_clusters_list , optional: true + tuple val(meta), path("all_SVs/breakpoint_clusters.tsv") , emit: all_breakpoints_clusters , optional: true + tuple val(meta), path("all_SVs/plots/severus_*.html") , emit: all_plots , optional: true + tuple val(meta), path("somatic_SVs/severus_somatic.vcf.gz") , emit: somatic_vcf //, optional: true + tuple val(meta), path("somatic_SVs/severus_somatic.vcf.gz.tbi") , emit: somatic_tbi , optional: true + tuple val(meta), path("somatic_SVs/breakpoint_clusters_list.tsv") , emit: somatic_breakpoints_clusters_list, optional: true + tuple val(meta), path("somatic_SVs/breakpoint_clusters.tsv") , emit: somatic_breakpoints_clusters , optional: true + tuple val(meta), path("somatic_SVs/plots/severus_*.html") , emit: somatic_plots , optional: true + path "versions.yml" , emit: versions + + +[2025-11-27 15:52:38,673] nf_core.components.nfcore_component [DEBUG ] Found 18 outputs in modules/nf-core/severus/main.nf +[2025-11-27 15:52:38,673] nf_core.components.nfcore_component [DEBUG ] Outputs: {'log': [[{'meta': {}}, {'severus.log': {}}]], 'read_qual': [[{'meta': {}}, {'read_qual.txt': {}}]], 'breakpoints_double': [[{'meta': {}}, {'breakpoints_double.csv': {}}]], 'read_alignments': [[{'meta': {}}, {'read_alignments': {}}]], 'read_ids': [[{'meta': {}}, {'read_ids.csv': {}}]], 'collapsed_dup': [[{'meta': {}}, {'severus_collaped_dup.bed': {}}]], 'loh': [[{'meta': {}}, {'severus_LOH.bed': {}}]], 'all_vcf': [[{'meta': {}}, {'all_SVs/severus_all.vcf.gz': {}}]], 'all_tbi': [[{'meta': {}}, {'all_SVs/severus_all.vcf.gz.tbi': {}}]], 'all_breakpoints_clusters_list': [[{'meta': {}}, {'all_SVs/breakpoint_clusters_list.tsv': {}}]], 'all_breakpoints_clusters': [[{'meta': {}}, {'all_SVs/breakpoint_clusters.tsv': {}}]], 'all_plots': [[{'meta': {}}, {'all_SVs/plots/severus_*.html': {}}]], 'somatic_vcf': [[{'meta': {}}, {'somatic_SVs/severus_somatic.vcf.gz': {}}]], 'somatic_tbi': [[{'meta': {}}, {'somatic_SVs/severus_somatic.vcf.gz.tbi': {}}]], 'somatic_breakpoints_clusters_list': [[{'meta': {}}, {'somatic_SVs/breakpoint_clusters_list.tsv': {}}]], 'somatic_breakpoints_clusters': [[{'meta': {}}, {'somatic_SVs/breakpoint_clusters.tsv': {}}]], 'somatic_plots': [[{'meta': {}}, {'somatic_SVs/plots/severus_*.html': {}}]], 'versions': [{'versions.yml': {}}]} +[2025-11-27 15:52:38,673] nf_core.components.nfcore_component [DEBUG ] Output data: + tuple val(meta), path("severus.log") , emit: log + tuple val(meta), path("read_qual.txt") , emit: read_qual + tuple val(meta), path("breakpoints_double.csv") , emit: breakpoints_double + tuple val(meta), path("read_alignments") , emit: read_alignments , optional: true + tuple val(meta), path("read_ids.csv") , emit: read_ids , optional: true + tuple val(meta), path("severus_collaped_dup.bed") , emit: collapsed_dup , optional: true + tuple val(meta), path("severus_LOH.bed") , emit: loh , optional: true + tuple val(meta), path("all_SVs/severus_all.vcf.gz") , emit: all_vcf , optional: true + tuple val(meta), path("all_SVs/severus_all.vcf.gz.tbi") , emit: all_tbi , optional: true + tuple val(meta), path("all_SVs/breakpoint_clusters_list.tsv") , emit: all_breakpoints_clusters_list , optional: true + tuple val(meta), path("all_SVs/breakpoint_clusters.tsv") , emit: all_breakpoints_clusters , optional: true + tuple val(meta), path("all_SVs/plots/severus_*.html") , emit: all_plots , optional: true + tuple val(meta), path("somatic_SVs/severus_somatic.vcf.gz") , emit: somatic_vcf //, optional: true + tuple val(meta), path("somatic_SVs/severus_somatic.vcf.gz.tbi") , emit: somatic_tbi , optional: true + tuple val(meta), path("somatic_SVs/breakpoint_clusters_list.tsv") , emit: somatic_breakpoints_clusters_list, optional: true + tuple val(meta), path("somatic_SVs/breakpoint_clusters.tsv") , emit: somatic_breakpoints_clusters , optional: true + tuple val(meta), path("somatic_SVs/plots/severus_*.html") , emit: somatic_plots , optional: true + path "versions.yml" , emit: versions + + +[2025-11-27 15:52:38,673] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/severus/main.nf +[2025-11-27 15:52:38,673] nf_core.components.nfcore_component [DEBUG ] Topics: {} +[2025-11-27 15:52:38,674] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:52:38,674] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:38,880] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:38,892] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:52:38,892] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:52:38,893] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:52:38,893] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:39,092] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:52:39,096] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/severus'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:39,097] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/severus'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:39,214] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:52:39,367] nf_core.components.components_differ [DEBUG ] Applying patch to modules/nf-core/severus/main.nf +[2025-11-27 15:52:39,367] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:52:39,368] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:39,435] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:39,448] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:52:39,448] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:52:39,449] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:52:39,449] git.cmd [DEBUG ] Popen(['git', 'checkout', '81880787133db07d9b4c1febd152c090eb8325dc'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:49,232] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:57,844] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/nf-core/untar/main.nf +[2025-11-27 15:52:57,844] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'archive': {}}]] +[2025-11-27 15:52:57,844] nf_core.components.nfcore_component [DEBUG ] Found output_data: + tuple val(meta), path("${prefix}"), emit: untar + path "versions.yml", emit: versions + + +[2025-11-27 15:52:57,844] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/nf-core/untar/main.nf +[2025-11-27 15:52:57,844] nf_core.components.nfcore_component [DEBUG ] Outputs: {'untar': [[{'meta': {}}, {'${prefix}': {}}]], 'versions': [{'versions.yml': {}}]} +[2025-11-27 15:52:57,844] nf_core.components.nfcore_component [DEBUG ] Output data: + tuple val(meta), path("${prefix}"), emit: untar + path "versions.yml", emit: versions + + +[2025-11-27 15:52:57,844] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/untar/main.nf +[2025-11-27 15:52:57,844] nf_core.components.nfcore_component [DEBUG ] Topics: {} +[2025-11-27 15:52:57,845] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:52:57,845] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:58,185] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:58,197] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:52:58,198] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:52:58,198] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:52:58,199] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:58,243] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:52:58,246] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/untar'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:58,247] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/untar'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:58,344] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:52:58,548] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:52:58,549] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:58,620] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:52:58,633] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:52:58,633] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:52:58,634] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:52:58,634] git.cmd [DEBUG ] Popen(['git', 'checkout', '41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:53:01,667] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:53:05,409] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/nf-core/unzip/main.nf +[2025-11-27 15:53:05,409] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'archive': {}}]] +[2025-11-27 15:53:05,409] nf_core.components.nfcore_component [DEBUG ] Found output_data: + tuple val(meta), path("${prefix}/"), emit: unzipped_archive + path "versions.yml" , emit: versions + + +[2025-11-27 15:53:05,409] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/nf-core/unzip/main.nf +[2025-11-27 15:53:05,409] nf_core.components.nfcore_component [DEBUG ] Outputs: {'unzipped_archive': [[{'meta': {}}, {'${prefix}/': {}}]], 'versions': [{'versions.yml': {}}]} +[2025-11-27 15:53:05,410] nf_core.components.nfcore_component [DEBUG ] Output data: + tuple val(meta), path("${prefix}/"), emit: unzipped_archive + path "versions.yml" , emit: versions + + +[2025-11-27 15:53:05,410] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/unzip/main.nf +[2025-11-27 15:53:05,410] nf_core.components.nfcore_component [DEBUG ] Topics: {} +[2025-11-27 15:53:05,410] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:53:05,411] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:53:05,637] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:53:05,649] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:53:05,649] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:53:05,649] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:53:05,650] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:53:05,794] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:53:05,798] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/unzip'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:53:05,799] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/unzip'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:53:05,893] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:53:06,081] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:53:06,082] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:53:06,193] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:53:06,205] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:53:06,205] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:53:06,206] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:53:06,206] git.cmd [DEBUG ] Popen(['git', 'checkout', '41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:53:09,447] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:53:13,327] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/nf-core/wget/main.nf +[2025-11-27 15:53:13,327] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'url': {}}]] +[2025-11-27 15:53:13,327] nf_core.components.nfcore_component [DEBUG ] Found output_data: + tuple val(meta), path("${prefix}.${suffix}"), emit: outfile + path "versions.yml" , emit: versions + + +[2025-11-27 15:53:13,327] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/nf-core/wget/main.nf +[2025-11-27 15:53:13,327] nf_core.components.nfcore_component [DEBUG ] Outputs: {'outfile': [[{'meta': {}}, {'${prefix}.${suffix}': {}}]], 'versions': [{'versions.yml': {}}]} +[2025-11-27 15:53:13,328] nf_core.components.nfcore_component [DEBUG ] Output data: + tuple val(meta), path("${prefix}.${suffix}"), emit: outfile + path "versions.yml" , emit: versions + + +[2025-11-27 15:53:13,328] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/wget/main.nf +[2025-11-27 15:53:13,328] nf_core.components.nfcore_component [DEBUG ] Topics: {} +[2025-11-27 15:53:13,328] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:53:13,328] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:53:13,447] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:53:13,458] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:53:13,459] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:53:13,459] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:53:13,460] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:53:13,563] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:53:13,567] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/nf-core/wget'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:53:13,568] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'modules/wget'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:53:13,684] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:53:13,841] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:53:13,842] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:53:13,932] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:53:13,943] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:53:13,944] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:53:13,944] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:53:13,944] git.cmd [DEBUG ] Popen(['git', 'checkout', '41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:53:16,975] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:53:21,106] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:53:21,107] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:53:21,393] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:53:21,417] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:53:21,418] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:53:21,418] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:53:21,420] git.cmd [DEBUG ] Popen(['git', 'checkout', '05954dab2ff481bcb999f24455da29a5828af08d'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:53:27,600] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:53:38,141] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:53:38,142] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:53:38,286] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:53:38,298] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:53:38,298] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:53:38,298] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:53:38,299] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:53:38,354] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:53:38,358] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'subworkflows/nf-core/bam_stats_samtools'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:53:38,372] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:53:38,458] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:53:38,459] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:53:38,517] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:53:38,528] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:53:38,529] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:53:38,529] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:53:38,530] git.cmd [DEBUG ] Popen(['git', 'checkout', 'c2b22d85f30a706a3073387f30380704fcae013b'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:53:51,273] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:54:04,283] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:54:04,285] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:54:05,104] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:54:05,146] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:54:05,149] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:54:05,150] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:54:05,154] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:54:05,466] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:54:05,484] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'subworkflows/nf-core/utils_nextflow_pipeline'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:54:05,611] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:54:05,766] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:54:05,768] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:54:05,968] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:54:06,009] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:54:06,011] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:54:06,012] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:54:06,013] git.cmd [DEBUG ] Popen(['git', 'checkout', '51ae5406a030d4da1e49e4dab49756844fdd6c7a'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:54:43,965] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:54:57,578] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:54:57,578] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:54:57,881] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:54:57,895] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:54:57,895] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:54:57,896] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:54:57,897] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:54:58,070] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:54:58,074] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'subworkflows/nf-core/utils_nfcore_pipeline'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:54:58,084] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:54:58,172] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:54:58,173] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:54:58,226] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:54:58,240] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:54:58,241] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:54:58,241] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:54:58,241] git.cmd [DEBUG ] Popen(['git', 'checkout', '2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:55:06,742] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:55:16,344] git.util [DEBUG ] sys.platform='linux', git_executable='git' +[2025-11-27 15:55:16,344] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:55:16,558] git.cmd [DEBUG ] Popen(['git', 'merge', 'origin/master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:55:16,572] nf_core.utils [DEBUG ] Got '/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules' as path +[2025-11-27 15:55:16,573] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json +[2025-11-27 15:55:16,573] nf_core.utils [DEBUG ] Using config file: /user/leuven/351/vsc35115/.config/nfcore/nf-core/modules/.nf-core.yml +[2025-11-27 15:55:16,574] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:55:16,711] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:55:16,716] git.cmd [DEBUG ] Popen(['git', 'rev-list', '0d75d9a1f328368e06ccc5474cd5553a51672979', '--', 'subworkflows/nf-core/utils_nfschema_plugin'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) +[2025-11-27 15:55:16,727] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) +[2025-11-27 15:55:16,820] nf_core.pipelines.lint [DEBUG ] Printing final results +[2025-11-27 15:55:16,821] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,821] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,821] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,821] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,821] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,821] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,821] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,821] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,821] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,822] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,822] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,822] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,822] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,822] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,822] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,822] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,822] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,822] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,823] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,823] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,823] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,823] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,823] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,823] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,823] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,823] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,823] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,823] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,823] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,823] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,824] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,824] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,824] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,824] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,824] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,824] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,824] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,824] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,824] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,824] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,825] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,825] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,825] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,825] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,825] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,825] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,825] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,825] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,825] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,825] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,825] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,825] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,825] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,825] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,825] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,825] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,826] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,826] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,826] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,826] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,826] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,826] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,826] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,826] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,826] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,826] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,826] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,826] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,826] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,826] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,827] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,827] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,827] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,827] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,827] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,827] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,827] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,827] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,827] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,827] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,828] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,828] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,828] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,828] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,828] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,828] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,828] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,828] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,828] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,828] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,828] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,828] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,828] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,828] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,828] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,829] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,829] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,829] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,829] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,829] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,829] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,829] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,829] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,829] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,829] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,829] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,829] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,829] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,829] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,829] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,830] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,830] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,830] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,830] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,830] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,830] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,830] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,830] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,830] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,830] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,830] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,830] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,830] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,830] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,830] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,830] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,830] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,830] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,830] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,830] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,831] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,831] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,831] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,831] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,831] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,831] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,831] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,831] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,831] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,831] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,831] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,831] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,831] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,832] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,832] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,832] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,832] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,832] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,832] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,832] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,832] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,832] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,832] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,832] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,832] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,832] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,832] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,832] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,832] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,832] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,833] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,833] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,833] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,833] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,833] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,833] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,833] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,833] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,833] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,833] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,833] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,833] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,833] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,833] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,833] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,833] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,833] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,833] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,833] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,833] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,834] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,834] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,834] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,834] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,834] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,834] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,834] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,834] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,834] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,834] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,835] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,835] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,835] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,835] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,835] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,835] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,835] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,835] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,835] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,835] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,835] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,835] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,835] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,835] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,835] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,835] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,835] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,836] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,836] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,836] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,839] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,839] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,839] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,839] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,839] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,839] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,839] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,839] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,839] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,839] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,840] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,840] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,840] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,840] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,840] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,840] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,840] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,840] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,840] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,840] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,840] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,840] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,840] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,840] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,840] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,840] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,840] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,840] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,840] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,841] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,841] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,841] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,841] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,841] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,841] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,841] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,841] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,841] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,841] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,841] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,842] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,842] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,842] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,842] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,842] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,842] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,842] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,842] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,842] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,842] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,842] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,842] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,842] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,842] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,842] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,842] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,842] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,842] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,842] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,842] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,843] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,843] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,843] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,843] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,843] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,843] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,843] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,843] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,843] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,843] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,843] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,844] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,844] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,844] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,844] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,844] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,844] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,844] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,844] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,844] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,844] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,844] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,844] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,844] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,844] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,844] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,844] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,844] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,844] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,844] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,845] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,845] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,845] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,845] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,845] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,845] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,845] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,845] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,845] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,845] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,845] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,845] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,846] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,846] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,846] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,846] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,846] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,846] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,846] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,846] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,846] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,846] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,846] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,846] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,846] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,846] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,846] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,846] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,846] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,846] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,847] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,847] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,847] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,847] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,847] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,847] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,847] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,847] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,847] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,847] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,847] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,847] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,847] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,847] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,847] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,847] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,847] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,847] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,848] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,848] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,848] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,848] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,848] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,848] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,848] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,848] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,848] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,848] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,848] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,848] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,849] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,849] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,849] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,849] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,849] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,849] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,849] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,849] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,849] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,849] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,849] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,849] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,849] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,849] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,849] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,849] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,849] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,849] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,849] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,849] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,850] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,850] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,850] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,850] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,850] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,850] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,850] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,850] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,850] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,850] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,850] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,850] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,850] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,850] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,850] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,850] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,851] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,851] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,851] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,851] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,851] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,851] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,851] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,851] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,851] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,851] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,851] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,851] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,851] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,851] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,852] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,852] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,852] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,852] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,852] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,852] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,852] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,852] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,852] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,852] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,852] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,852] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,852] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,852] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,852] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,852] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,852] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,852] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,852] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,853] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,853] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,853] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,853] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,853] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,853] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,853] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,853] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,853] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,853] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,853] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,854] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,854] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,854] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,854] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,854] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,854] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,854] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,854] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,854] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,854] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,854] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,854] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,854] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,854] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,854] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,854] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,854] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,854] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,854] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,854] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,855] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,855] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,855] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,855] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,855] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,855] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,855] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,855] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,855] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,855] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,855] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,855] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,855] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,855] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,855] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,855] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,856] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,856] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,856] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,856] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,856] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,856] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,856] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,856] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,856] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,856] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,856] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,856] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,856] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,856] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,857] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,857] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,857] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,857] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,857] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,857] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,857] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,857] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,857] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,857] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,857] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,857] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,857] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,857] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,857] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,857] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,857] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,857] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,857] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,858] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,858] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,858] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,858] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,858] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,858] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,858] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,858] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,858] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,858] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,858] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,858] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,859] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,859] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,859] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,859] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,859] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,859] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,859] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,859] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,859] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,859] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,859] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,859] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,859] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,859] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,859] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,859] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,859] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,859] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,859] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,860] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,860] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,860] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,860] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,860] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,860] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,860] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,860] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,860] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,860] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,860] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,860] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,860] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,860] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,860] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,860] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,860] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,861] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,861] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,861] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,861] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,861] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,861] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,861] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,861] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,861] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,861] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,861] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,861] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,861] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,862] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,862] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,862] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,862] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,862] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,862] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,862] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,862] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,862] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,862] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,862] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,862] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,862] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,862] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,862] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,862] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,862] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,863] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,863] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,863] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,863] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,863] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,863] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,863] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,863] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,863] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,863] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,863] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,863] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,863] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,864] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,864] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,864] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,864] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,864] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,864] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,864] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,864] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,864] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,864] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,864] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,864] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,864] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,864] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,864] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,864] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,864] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,864] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,864] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,864] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,865] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,865] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,865] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,865] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,865] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,865] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,865] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,865] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,865] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,865] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,865] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,865] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,865] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,865] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,866] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,866] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,866] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,866] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,866] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,866] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,866] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,866] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,866] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,866] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,866] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,866] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,866] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,866] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,866] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,866] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,867] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,867] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,867] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,867] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,867] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,867] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,867] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,867] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,867] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,867] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,867] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,867] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,867] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,867] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,867] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,867] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,867] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,867] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,867] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,867] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,868] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,868] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,868] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,868] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,868] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,868] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,868] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,868] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,868] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,868] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,869] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,869] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,869] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,869] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,869] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,869] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,869] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,869] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,869] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,869] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,869] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,869] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,869] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,869] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,869] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,869] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,869] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,869] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,869] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,869] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,870] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,870] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,870] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,870] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,870] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,870] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,870] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,870] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,870] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,870] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,870] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,870] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,871] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,871] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,871] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,871] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,871] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,871] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,871] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,871] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,871] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,871] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,871] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,871] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,871] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,871] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,871] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,871] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,871] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,871] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,872] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,872] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,872] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,872] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,872] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,872] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,872] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,872] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,872] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,872] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,872] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,872] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,872] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,872] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,872] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,872] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,872] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,872] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,872] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,872] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,873] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,873] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,873] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,873] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,873] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,873] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,873] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,873] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,873] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,873] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,873] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,874] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,874] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,874] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,874] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,874] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,874] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,874] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,874] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,874] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,874] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,874] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,874] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,874] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,874] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,874] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,874] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,874] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,874] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,874] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,875] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,875] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,875] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,875] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,875] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,875] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,875] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,875] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,875] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,875] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,875] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,875] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,875] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,875] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,875] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,876] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,876] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,876] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,876] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,876] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,876] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,876] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,876] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,876] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,876] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,876] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,876] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,876] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,876] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,876] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,877] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,877] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,877] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,877] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,877] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,877] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,877] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,877] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,877] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,877] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,877] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,877] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,877] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,877] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,877] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,877] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,877] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,877] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,877] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,877] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,878] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,878] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,878] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,878] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,878] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,878] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,878] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,878] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,878] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,878] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,878] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,878] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,879] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,879] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,879] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,879] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,879] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,879] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,879] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,879] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,879] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,879] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,879] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,879] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,879] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,879] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,879] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,879] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,879] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,879] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,880] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,880] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,880] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,880] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,880] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,880] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,880] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,880] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,880] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,880] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,880] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,880] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,881] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,881] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,881] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,881] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,881] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,881] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,881] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,881] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,881] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,881] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,881] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,881] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,881] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,881] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,881] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,881] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,881] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,881] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,882] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,882] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,882] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,882] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,882] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,882] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,882] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,882] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,882] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,882] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,882] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,882] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,882] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,882] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,882] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,882] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,882] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,882] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,882] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,882] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,883] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,883] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,883] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,883] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,883] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,883] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,883] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,883] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,883] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,883] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,883] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,884] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,884] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,884] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,884] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,884] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,884] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,884] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,884] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,884] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,884] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,884] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,884] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,884] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,884] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,884] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,884] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,884] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,884] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,884] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,885] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,885] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,885] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,885] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,885] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,885] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,885] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,885] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,885] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,885] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,886] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,886] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,886] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,886] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,886] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,886] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,886] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,886] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,886] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,886] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,886] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,886] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,886] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,886] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,886] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,886] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,886] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,887] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,887] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,887] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,887] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,887] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,887] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,887] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,887] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,887] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,887] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,887] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,887] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,887] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,888] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,888] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,888] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,888] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,888] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,888] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,888] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,888] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,888] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,888] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,888] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,888] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,888] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,888] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,888] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,888] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,888] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,888] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,888] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,888] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,889] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,889] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,889] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,889] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,889] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,889] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,889] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,889] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,889] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,889] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,889] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,889] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,889] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,889] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,890] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,890] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,890] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,890] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,890] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,890] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,890] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,890] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,890] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,890] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,890] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,890] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,890] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,890] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,890] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,890] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,891] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,891] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,891] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,891] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,891] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,891] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,891] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,891] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,891] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,891] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,891] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,891] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,891] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,891] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,891] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,891] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,891] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,891] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,891] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,891] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,892] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,892] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,892] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,892] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,892] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,892] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,892] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,892] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,892] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,892] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,893] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,893] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,893] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,893] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,893] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,893] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,893] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,893] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,893] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,893] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,893] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,893] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,893] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,893] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,893] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,893] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,893] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,893] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,893] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,893] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,894] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,894] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,894] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,894] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,894] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,894] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,894] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,894] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,894] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,894] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,894] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,894] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,894] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,894] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,894] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,895] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,895] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,895] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,895] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,895] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,895] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,895] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,895] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,895] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,895] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,895] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,895] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,895] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,895] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,895] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,896] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,896] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,896] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,896] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,896] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,896] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,896] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,896] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,896] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,896] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,896] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,896] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,896] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,896] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,896] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,896] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,896] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,896] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,896] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,896] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,897] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,897] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,897] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,897] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,897] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,897] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,897] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,897] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,897] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,897] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,898] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,898] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,898] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,898] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,898] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,898] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,898] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,898] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,898] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,898] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,898] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,898] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,898] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,898] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,898] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,898] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,898] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,898] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,898] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,898] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,899] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,899] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,899] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,899] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,899] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,899] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,899] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,899] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,899] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,899] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,899] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,899] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,899] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,899] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,900] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,900] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,900] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,900] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,900] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,900] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,900] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,900] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,900] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,900] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,900] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,900] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,900] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,900] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,900] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,900] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,901] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,901] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,901] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,901] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,901] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,901] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,901] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,901] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,901] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,901] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,901] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,901] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,901] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,901] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,901] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,901] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,901] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,901] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,901] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,901] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,902] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,902] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,902] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,902] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,902] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,902] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,902] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,902] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,902] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,902] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,902] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,903] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,903] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,903] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,903] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,903] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,903] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,903] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,903] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,903] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,903] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,903] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,903] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,903] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,903] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,903] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,903] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,903] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,903] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,903] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,904] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,904] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,904] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,904] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,904] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,904] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,904] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,904] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,904] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,904] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,904] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,904] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,904] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,904] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,905] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,905] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,905] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,905] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,905] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,905] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,905] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,905] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,905] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,905] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,905] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,905] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,905] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,905] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,905] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,905] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,906] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,906] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,906] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,906] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,906] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,906] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,906] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,906] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,906] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,906] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,906] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,906] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,906] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,906] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,906] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,906] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,906] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,906] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,906] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,906] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,907] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,907] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,907] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,907] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,907] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,907] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,907] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,907] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,907] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,907] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,907] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,907] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,908] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,908] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,908] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,908] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,908] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,908] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,908] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,908] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,908] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,908] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,908] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,908] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,908] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,908] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,908] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,908] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,908] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,908] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,909] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,909] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,909] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,909] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,909] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,909] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,909] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,909] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,909] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,909] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,909] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,909] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,909] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,909] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,909] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,909] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,910] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,910] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,910] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,910] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,910] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,910] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,910] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,910] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,910] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,910] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,910] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,910] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,910] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,910] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,911] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,911] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,911] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,911] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,911] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,911] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,911] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,911] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,911] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,911] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,911] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,911] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,911] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,911] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,911] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,911] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,911] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,911] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,911] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,911] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,912] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,912] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,912] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,912] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,912] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,912] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,912] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,912] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,912] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,912] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,912] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,912] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,912] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,912] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,913] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,913] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,913] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,913] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,913] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,913] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,913] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,913] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,913] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,913] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,913] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,913] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,913] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,913] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,913] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,913] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,914] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,914] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,914] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,914] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,914] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,914] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,914] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,914] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,914] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,914] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,914] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,914] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,914] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,914] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,914] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,914] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,914] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,914] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,914] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,914] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,915] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,915] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,915] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,915] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,915] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,915] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,915] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,915] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,915] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,915] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,916] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,916] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,916] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,916] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,916] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,916] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,916] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,916] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,916] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,916] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,916] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,916] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,916] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,916] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,916] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,916] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,916] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,916] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,916] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,916] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,917] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,917] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,917] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,917] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,917] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,917] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,917] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,917] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,917] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,917] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,917] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,917] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,917] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,917] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,917] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,917] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,918] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,918] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,918] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,918] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,918] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,918] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,918] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,918] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,918] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,918] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,918] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,918] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,918] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,918] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,919] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,919] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,919] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,919] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,919] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,919] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,919] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,919] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,919] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,919] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,919] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,919] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,919] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,919] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,919] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,919] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,919] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,919] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,919] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,919] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,920] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,920] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,920] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,920] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,920] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,920] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,920] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,920] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,920] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,920] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,920] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,920] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,920] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,920] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,920] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,920] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,921] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,921] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,921] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,921] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,921] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,921] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,921] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,921] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,921] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,921] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,921] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,921] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,921] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,921] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,922] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,922] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,922] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,922] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,922] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,922] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,922] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,922] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,922] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,922] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,922] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,922] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,922] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,922] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,922] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,922] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,922] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,922] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,922] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,922] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,923] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,923] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,923] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,923] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,923] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,923] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,923] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,923] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,923] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,923] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,923] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,924] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,924] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,924] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,924] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,924] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,924] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,924] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,924] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,924] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,924] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,924] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,924] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,924] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,924] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,924] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,924] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,924] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,924] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,924] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,925] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,925] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,925] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,925] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,925] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,925] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,925] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,925] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,925] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,925] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,925] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,925] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,925] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,925] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,925] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,925] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,925] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,926] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,926] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,926] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,926] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,926] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,926] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,926] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,926] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,926] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,926] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,926] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,926] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,926] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,927] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,927] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,927] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,927] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,927] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,927] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,927] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,927] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,927] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,927] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,927] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,927] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,927] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,927] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,927] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,927] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,927] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,927] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,927] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,927] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,947] nf_core.components.lint [DEBUG ] Printing final results +[2025-11-27 15:55:16,948] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,948] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,948] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,948] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,948] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,948] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,948] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,948] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,948] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,948] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,949] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,949] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,949] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,949] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,949] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,949] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,949] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,949] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,949] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,949] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,949] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,949] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,949] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,949] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,949] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,949] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,949] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,949] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,949] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,949] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,950] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,950] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,950] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,950] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,950] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,950] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,950] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,950] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,950] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,950] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,951] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,951] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,951] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,951] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,951] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,951] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,951] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,951] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,951] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,951] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,951] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,951] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,951] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,951] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,951] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,951] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,951] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,951] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,951] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,951] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,952] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,952] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,952] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,952] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,952] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,952] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,952] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,952] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,952] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,952] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,952] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,952] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,952] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,952] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,952] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,952] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,953] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,953] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,953] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,953] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,953] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,953] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,953] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,953] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,953] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,953] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,953] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,953] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,953] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,953] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,954] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,954] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,954] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,954] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,954] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,954] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,954] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,954] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,954] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,954] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,954] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,954] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,954] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,954] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,954] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,954] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,954] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,954] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,954] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,954] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,955] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,955] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,955] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,955] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,955] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,955] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,955] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,955] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,955] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,955] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,956] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,956] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,956] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,956] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,956] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,956] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,956] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,956] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,956] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,956] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,956] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,956] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,956] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,956] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,956] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,956] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,956] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,956] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,956] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,956] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,957] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,957] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,957] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,957] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,957] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,957] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,957] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,957] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,957] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,957] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,958] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,958] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,958] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,958] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,958] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,958] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,958] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,958] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,958] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,958] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,958] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,958] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,958] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,958] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,958] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,958] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,958] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,958] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,958] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,958] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,959] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,959] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,959] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,959] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,959] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,959] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,959] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,959] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,959] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,959] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,959] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,959] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,959] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,959] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,959] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,959] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,960] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,960] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,960] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,960] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,968] nf_core.components.lint [DEBUG ] Printing final results +[2025-11-27 15:55:16,969] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,969] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,969] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,969] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,969] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,969] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,969] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,969] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,969] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,969] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,970] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,970] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,970] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,970] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,970] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,970] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,970] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,970] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,970] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,970] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,970] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,970] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,970] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,970] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,970] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,971] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,971] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,971] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,971] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,971] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,971] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,971] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,971] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,971] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,971] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,971] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,971] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,971] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,971] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,971] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,972] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,972] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,972] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,972] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,972] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,972] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,972] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,972] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,972] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,972] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,972] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,972] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,972] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,972] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,972] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,972] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,972] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,972] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,973] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,973] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,973] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,973] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,973] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,973] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,973] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,973] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,973] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,973] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,973] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,973] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,974] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,974] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,974] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,974] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,974] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,974] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,974] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,974] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,974] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,974] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,974] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,974] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,974] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,974] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,974] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,974] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,974] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,974] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,974] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,975] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,975] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,975] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,975] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,975] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,975] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,975] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,975] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,975] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,975] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,975] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,976] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,976] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,976] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,976] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,976] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,976] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,976] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,976] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,976] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,976] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,976] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,976] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,976] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,976] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,976] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,976] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,976] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,977] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,977] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,977] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,977] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,977] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,977] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,977] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,977] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,977] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,977] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,977] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,977] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,977] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,978] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,978] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,978] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,978] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,978] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,978] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,978] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,978] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,978] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,978] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,978] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,978] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,978] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,978] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,978] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,978] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,978] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,978] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,978] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,978] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,979] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,979] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,979] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,979] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,979] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,979] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,979] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,979] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,979] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,979] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,980] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,980] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,980] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,980] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,980] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,980] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,980] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,980] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,980] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,980] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,980] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,980] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,980] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,980] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,980] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,980] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,980] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,980] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,980] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,980] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,981] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,981] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,981] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,981] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,981] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,981] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,981] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,981] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,981] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,981] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,982] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,982] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,982] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,982] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,982] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,982] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,982] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,982] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,982] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,982] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,982] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,982] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,982] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,982] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,982] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,982] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,982] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,982] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,982] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,982] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,983] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,983] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,983] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,983] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,983] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,983] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,983] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,983] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,983] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,983] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,984] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,984] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,984] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,984] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,984] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,984] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,984] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,984] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,984] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,984] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,984] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,984] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,984] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,984] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,984] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,984] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,984] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,984] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,984] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,984] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,985] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,985] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,985] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,985] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,985] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,985] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,985] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,985] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,985] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,985] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,986] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,986] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,986] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,986] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,986] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,986] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,986] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,986] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,986] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,986] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,986] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,986] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,986] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,986] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,986] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,986] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,986] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,986] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,986] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,986] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,987] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,987] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,987] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,987] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,987] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,987] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,987] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,987] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,987] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,987] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,988] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,988] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,988] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,988] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,988] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,988] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,988] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,988] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,988] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,988] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,988] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,988] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,988] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,988] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,988] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,988] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,988] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,988] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,988] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,988] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,989] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,989] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,989] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,989] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,989] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,989] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,989] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,989] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,989] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,989] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,990] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,990] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,990] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,990] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,990] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,990] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,990] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,990] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,990] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,990] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,990] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,990] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,990] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,990] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,990] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,990] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,990] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,990] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,990] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,990] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,991] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,991] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,991] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,991] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,991] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,991] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,991] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,991] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,991] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,991] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,992] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,992] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,992] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,992] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,992] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,992] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,992] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,992] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,992] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,992] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,992] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,992] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,992] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,992] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,992] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,992] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,992] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,992] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,992] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,992] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,993] markdown_it.rules_block.code [DEBUG ] entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,993] markdown_it.rules_block.fence [DEBUG ] entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,993] markdown_it.rules_block.blockquote [DEBUG ] entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,993] markdown_it.rules_block.hr [DEBUG ] entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,993] markdown_it.rules_block.list [DEBUG ] entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,993] markdown_it.rules_block.reference [DEBUG ] entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,993] markdown_it.rules_block.html_block [DEBUG ] entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,993] markdown_it.rules_block.heading [DEBUG ] entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,993] markdown_it.rules_block.lheading [DEBUG ] entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False +[2025-11-27 15:55:16,993] markdown_it.rules_block.paragraph [DEBUG ] entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False diff --git a/subworkflows/local/tumor_normal_happhase.nf b/subworkflows/local/tumor_normal_happhase.nf index 678f1cd6..923c22a5 100644 --- a/subworkflows/local/tumor_normal_happhase.nf +++ b/subworkflows/local/tumor_normal_happhase.nf @@ -55,7 +55,7 @@ workflow TUMOR_NORMAL_HAPPHASE { return [ basecall_model, new_meta, bam, bai ] } .set { normal_bams_model } - + normal_bams_model .combine(downloaded_model_files,by:0) @@ -114,7 +114,7 @@ workflow TUMOR_NORMAL_HAPPHASE { return [meta, bam, bai, vcf, svs, mods] } .set{ normal_bams_germlinevcf } - + // normal_bams -> meta: [id, paired_data, platform, sex, type, fiber, basecall_model] // bam: list of concatenated aligned bams @@ -281,7 +281,7 @@ workflow TUMOR_NORMAL_HAPPHASE { CLAIRS.out.vcfs .join(CLAIRS.out.tbi) .set{clairs_out} - + BCFTOOLS_CONCAT( clairs_out ) From ca04e17373a001f30a6758f18c18acf73f93f191 Mon Sep 17 00:00:00 2001 From: robert-a-forsyth Date: Thu, 27 Nov 2025 16:01:26 +0100 Subject: [PATCH 38/42] fix log --- lint_log.txt | 284 +++++++++++++++++++++++++-------------------------- 1 file changed, 142 insertions(+), 142 deletions(-) diff --git a/lint_log.txt b/lint_log.txt index 5e087cd0..366aea19 100644 --- a/lint_log.txt +++ b/lint_log.txt @@ -17,7 +17,7 @@ [2025-11-27 15:47:40,379] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json [2025-11-27 15:47:40,379] nf_core.utils [DEBUG ] Using config file: .nf-core.yml [2025-11-27 15:47:41,648] nf_core.pipelines.lint_utils [DEBUG ] The following files were modified by prettier: - + modules.json @@ -34,7 +34,7 @@ modules.json [2025-11-27 15:47:41,727] nf_core.utils [DEBUG ] Found a config cache, loading: /user/leuven/351/vsc35115/.nextflow/nf-core/wf-config-cache-1e87c6c5537e627bca015c3d8.json [2025-11-27 15:47:41,728] nf_core.utils [DEBUG ] Using config file: .nf-core.yml [2025-11-27 15:47:42,155] nf_core.pipelines.lint_utils [DEBUG ] The following files were modified by prettier: - + modules.json @@ -130,7 +130,7 @@ modules.json [2025-11-27 15:50:36,563] nf_core.pipelines.lint [DEBUG ] Running lint test: rocrate_readme_sync [2025-11-27 15:50:36,566] nf_core.components.nfcore_component [DEBUG ] Found 2 inputs in modules/local/wakhan/main.nf [2025-11-27 15:50:36,566] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'tumor_input': {}}, {'tumor_index': {}}, {'normal_input': {}}, {'normal_index': {}}, {'vcf': {}}, {'breakpoints': {}}], [{'meta2': {}}, {'reference': {}}]] -[2025-11-27 15:50:36,566] nf_core.components.nfcore_component [DEBUG ] Found output_data: +[2025-11-27 15:50:36,566] nf_core.components.nfcore_component [DEBUG ] Found output_data: tuple val(meta), path("*/*_genes_genome.html") , emit: genes_genome_html tuple val(meta), path("*/*_genes_genome.pdf") , emit: genes_genome_pdf tuple val(meta), path("*/*_genome_copynumbers_breakpoints.html") , emit: breakpoints_html @@ -156,10 +156,10 @@ modules.json tuple val(meta), path("solutions_ranks.tsv") , emit: solutions_ranks path "versions.yml" , emit: versions - + [2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Found 24 outputs in modules/local/wakhan/main.nf [2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Outputs: {'genes_genome_html': [[{'meta': {}}, {'*/*_genes_genome.html': {}}]], 'genes_genome_pdf': [[{'meta': {}}, {'*/*_genes_genome.pdf': {}}]], 'breakpoints_html': [[{'meta': {}}, {'*/*_genome_copynumbers_breakpoints.html': {}}]], 'breakpoints_pdf': [[{'meta': {}}, {'*/*_genome_copynumbers_breakpoints.pdf': {}}]], 'breakpoints_subclonal_html': [[{'meta': {}}, {'*/*_genome_copynumbers_breakpoints_subclonal.html': {}}]], 'breakpoints_subclonal_pdf': [[{'meta': {}}, {'*/*_genome_copynumbers_breakpoints_subclonal.pdf': {}}]], 'copynumbers_details_html': [[{'meta': {}}, {'*/*_genome_copynumbers_details.html': {}}]], 'copynumbers_details_pdf': [[{'meta': {}}, {'*/*_genome_copynumbers_details.pdf': {}}]], 'bed_files': [[{'meta': {}}, {'*/bed_output/*.bed': {}}]], 'variation_plots': [[{'meta': {}}, {'*/variation_plots/*.html': {}}]], 'vcf_files': [[{'meta': {}}, {'*/vcf_output/*_wakhan_cna_*.vcf': {}}]], 'heatmap_html': [[{'meta': {}}, {'*_heatmap_ploidy_purity.html': {}}]], 'heatmap_pdf': [[{'meta': {}}, {'*_heatmap_ploidy_purity.html.pdf': {}}]], 'optimized_peak_html': [[{'meta': {}}, {'*_optimized_peak.html': {}}]], 'coverage_csv': [[{'meta': {}}, {'coverage_data/*.csv': {}}]], 'coverage_plots_html': [[{'meta': {}}, {'coverage_plots/*.html': {}}]], 'coverage_plots_pdf': [[{'meta': {}}, {'coverage_plots/*.pdf': {}}]], 'phasing_html': [[{'meta': {}}, {'phasing_output/*.html': {}}]], 'phasing_pdf': [[{'meta': {}}, {'phasing_output/*.pdf': {}}]], 'rephased_vcf': [[{'meta': {}}, {'phasing_output/*.rephased.vcf.gz': {}}]], 'rephased_vcf_index': [[{'meta': {}}, {'phasing_output/*.rephased.vcf.gz.csi': {}}]], 'snps_loh_plot': [[{'meta': {}}, {'snps_loh_plots/*_genome_snps_ratio_loh.html': {}}]], 'solutions_ranks': [[{'meta': {}}, {'solutions_ranks.tsv': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Output data: +[2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Output data: tuple val(meta), path("*/*_genes_genome.html") , emit: genes_genome_html tuple val(meta), path("*/*_genes_genome.pdf") , emit: genes_genome_pdf tuple val(meta), path("*/*_genome_copynumbers_breakpoints.html") , emit: breakpoints_html @@ -185,164 +185,164 @@ modules.json tuple val(meta), path("solutions_ranks.tsv") , emit: solutions_ranks path "versions.yml" , emit: versions - + [2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/local/wakhan/main.nf [2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Topics: {} [2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Found 3 inputs in modules/local/clairs/main.nf [2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'tumor_bam': {}}, {'tumor_bai': {}}, {'normal_bam': {}}, {'normal_bai': {}}, {'model': {}}], [{'meta2': {}}, {'reference': {}}], [{'meta3': {}}, {'index': {}}]] -[2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Found output_data: +[2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Found output_data: tuple val(meta), path("*.vcf.gz"), emit: vcfs tuple val(meta), path("*.vcf.gz.tbi"), emit: tbi path "versions.yml", emit: versions - + [2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Found 3 outputs in modules/local/clairs/main.nf [2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Outputs: {'vcfs': [[{'meta': {}}, {'*.vcf.gz': {}}]], 'tbi': [[{'meta': {}}, {'*.vcf.gz.tbi': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Output data: +[2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Output data: tuple val(meta), path("*.vcf.gz"), emit: vcfs tuple val(meta), path("*.vcf.gz.tbi"), emit: tbi path "versions.yml", emit: versions - + [2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/local/clairs/main.nf [2025-11-27 15:50:36,567] nf_core.components.nfcore_component [DEBUG ] Topics: {} [2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/local/cramino/main.nf [2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'bam': {}}]] -[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Found output_data: +[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Found output_data: tuple val(meta), path("*.txt"), emit: txt path "versions.yml" , emit: versions - + [2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/local/cramino/main.nf [2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Outputs: {'txt': [[{'meta': {}}, {'*.txt': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Output data: +[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Output data: tuple val(meta), path("*.txt"), emit: txt path "versions.yml" , emit: versions - + [2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/local/cramino/main.nf [2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Topics: {} [2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/local/metaextract/main.nf [2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'bam': {}}]] -[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Found output_data: +[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Found output_data: tuple val(meta), env(basecall_model), env(kinetics) , emit: meta_ext path "versions.yml" , emit: versions - + [2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/local/metaextract/main.nf [2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Outputs: {'meta_ext': [[{'meta': {}}, {'basecall_model': {}}, {'kinetics': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Output data: +[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Output data: tuple val(meta), env(basecall_model), env(kinetics) , emit: meta_ext path "versions.yml" , emit: versions - + [2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/local/metaextract/main.nf [2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Topics: {} [2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Found 7 inputs in modules/local/clairsto/main.nf [2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'tumor_bam': {}}, {'tumor_bai': {}}, {'model': {}}], [{'meta2': {}}, {'reference': {}}], [{'meta3': {}}, {'index': {}}], {'dbSNP': {}}, {'colors': {}}, {'onekgenomes': {}}, {'gnomad': {}}] -[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Found output_data: +[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Found output_data: tuple val(meta), path("indel.vcf.gz"), emit: indel_vcf tuple val(meta), path("indel.vcf.gz.tbi"), emit: indel_tbi tuple val(meta), path("snv.vcf.gz"), emit: snv_vcf tuple val(meta), path("snv.vcf.gz.tbi"), emit: snv_tbi path "versions.yml", emit: versions - + [2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Found 5 outputs in modules/local/clairsto/main.nf [2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Outputs: {'indel_vcf': [[{'meta': {}}, {'indel.vcf.gz': {}}]], 'indel_tbi': [[{'meta': {}}, {'indel.vcf.gz.tbi': {}}]], 'snv_vcf': [[{'meta': {}}, {'snv.vcf.gz': {}}]], 'snv_tbi': [[{'meta': {}}, {'snv.vcf.gz.tbi': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Output data: +[2025-11-27 15:50:36,568] nf_core.components.nfcore_component [DEBUG ] Output data: tuple val(meta), path("indel.vcf.gz"), emit: indel_vcf tuple val(meta), path("indel.vcf.gz.tbi"), emit: indel_tbi tuple val(meta), path("snv.vcf.gz"), emit: snv_vcf tuple val(meta), path("snv.vcf.gz.tbi"), emit: snv_tbi path "versions.yml", emit: versions - + [2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/local/clairsto/main.nf [2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Topics: {} [2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/local/fibertoolsrs/fire/main.nf [2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'bam': {}}]] -[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Found output_data: +[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Found output_data: // TODO nf-core: Named file extensions MUST be emitted for ALL output channels tuple val(meta), path("*.bam"), emit: bam // TODO nf-core: List additional required output channels/values here path "versions.yml" , emit: versions - + [2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/local/fibertoolsrs/fire/main.nf [2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Outputs: {'bam': [[{'meta': {}}, {'*.bam': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Output data: +[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Output data: // TODO nf-core: Named file extensions MUST be emitted for ALL output channels tuple val(meta), path("*.bam"), emit: bam // TODO nf-core: List additional required output channels/values here path "versions.yml" , emit: versions - + [2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/local/fibertoolsrs/fire/main.nf [2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Topics: {} [2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/local/fibertoolsrs/predictm6a/main.nf [2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'bam': {}}]] -[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Found output_data: +[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Found output_data: // TODO nf-core: Named file extensions MUST be emitted for ALL output channels tuple val(meta), path("*.bam"), emit: bam // TODO nf-core: List additional required output channels/values here path "versions.yml" , emit: versions - + [2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/local/fibertoolsrs/predictm6a/main.nf [2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Outputs: {'bam': [[{'meta': {}}, {'*.bam': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Output data: +[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Output data: // TODO nf-core: Named file extensions MUST be emitted for ALL output channels tuple val(meta), path("*.bam"), emit: bam // TODO nf-core: List additional required output channels/values here path "versions.yml" , emit: versions - + [2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/local/fibertoolsrs/predictm6a/main.nf [2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Topics: {} [2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/local/fibertoolsrs/qc/main.nf [2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'bam': {}}]] -[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Found output_data: +[2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Found output_data: // TODO nf-core: Named file extensions MUST be emitted for ALL output channels tuple val(meta), path("*.txt"), emit: qc_txt // TODO nf-core: List additional required output channels/values here path "versions.yml" , emit: versions - + [2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/local/fibertoolsrs/qc/main.nf [2025-11-27 15:50:36,569] nf_core.components.nfcore_component [DEBUG ] Outputs: {'qc_txt': [[{'meta': {}}, {'*.txt': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Output data: +[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Output data: // TODO nf-core: Named file extensions MUST be emitted for ALL output channels tuple val(meta), path("*.txt"), emit: qc_txt // TODO nf-core: List additional required output channels/values here path "versions.yml" , emit: versions - + [2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/local/fibertoolsrs/qc/main.nf [2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Topics: {} [2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/local/fibertoolsrs/nucleosomes/main.nf [2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'bam': {}}]] -[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Found output_data: +[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Found output_data: // TODO nf-core: Named file extensions MUST be emitted for ALL output channels tuple val(meta), path("*.bam"), emit: bam // TODO nf-core: List additional required output channels/values here path "versions.yml" , emit: versions - + [2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/local/fibertoolsrs/nucleosomes/main.nf [2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Outputs: {'bam': [[{'meta': {}}, {'*.bam': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Output data: +[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Output data: // TODO nf-core: Named file extensions MUST be emitted for ALL output channels tuple val(meta), path("*.bam"), emit: bam // TODO nf-core: List additional required output channels/values here path "versions.yml" , emit: versions - + [2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/local/fibertoolsrs/nucleosomes/main.nf [2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Topics: {} [2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/local/vcfsplit/main.nf [2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'snv_vcf': {}}, {'indel_vcf': {}}]] -[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Found output_data: +[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Found output_data: tuple val(meta), path("*somatic.vcf.gz") , emit: somatic_vcf tuple val(meta), path("*somatic.vcf.gz.tbi") , emit: somatic_tbi tuple val(meta), path("*germline.vcf.gz") , emit: germline_vcf @@ -350,10 +350,10 @@ modules.json path "versions.yml" , emit: versions - + [2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Found 5 outputs in modules/local/vcfsplit/main.nf [2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Outputs: {'somatic_vcf': [[{'meta': {}}, {'*somatic.vcf.gz': {}}]], 'somatic_tbi': [[{'meta': {}}, {'*somatic.vcf.gz.tbi': {}}]], 'germline_vcf': [[{'meta': {}}, {'*germline.vcf.gz': {}}]], 'germline_tbi': [[{'meta': {}}, {'*germline.vcf.gz.tbi': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Output data: +[2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Output data: tuple val(meta), path("*somatic.vcf.gz") , emit: somatic_vcf tuple val(meta), path("*somatic.vcf.gz.tbi") , emit: somatic_tbi tuple val(meta), path("*germline.vcf.gz") , emit: germline_vcf @@ -361,34 +361,34 @@ modules.json path "versions.yml" , emit: versions - + [2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/local/vcfsplit/main.nf [2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Topics: {} [2025-11-27 15:50:36,570] nf_core.components.nfcore_component [DEBUG ] Found 3 inputs in modules/local/clair3/main.nf [2025-11-27 15:50:36,571] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'bam': {}}, {'bai': {}}, {'model': {}}, {'platform': {}}], [{'meta2': {}}, {'reference': {}}], [{'meta3': {}}, {'index': {}}]] -[2025-11-27 15:50:36,571] nf_core.components.nfcore_component [DEBUG ] Found output_data: +[2025-11-27 15:50:36,571] nf_core.components.nfcore_component [DEBUG ] Found output_data: tuple val(meta), path("*merge_output.vcf.gz"), emit: vcf tuple val(meta), path("*merge_output.vcf.gz.tbi"), emit: tbi tuple val(meta), path("*phased_merge_output.vcf.gz"), emit: phased_vcf, optional: true tuple val(meta), path("*phased_merge_output.vcf.gz.tbi"), emit: phased_tbi, optional: true path "versions.yml", emit: versions - + [2025-11-27 15:50:36,571] nf_core.components.nfcore_component [DEBUG ] Found 5 outputs in modules/local/clair3/main.nf [2025-11-27 15:50:36,571] nf_core.components.nfcore_component [DEBUG ] Outputs: {'vcf': [[{'meta': {}}, {'*merge_output.vcf.gz': {}}]], 'tbi': [[{'meta': {}}, {'*merge_output.vcf.gz.tbi': {}}]], 'phased_vcf': [[{'meta': {}}, {'*phased_merge_output.vcf.gz': {}}]], 'phased_tbi': [[{'meta': {}}, {'*phased_merge_output.vcf.gz.tbi': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:50:36,571] nf_core.components.nfcore_component [DEBUG ] Output data: +[2025-11-27 15:50:36,571] nf_core.components.nfcore_component [DEBUG ] Output data: tuple val(meta), path("*merge_output.vcf.gz"), emit: vcf tuple val(meta), path("*merge_output.vcf.gz.tbi"), emit: tbi tuple val(meta), path("*phased_merge_output.vcf.gz"), emit: phased_vcf, optional: true tuple val(meta), path("*phased_merge_output.vcf.gz.tbi"), emit: phased_tbi, optional: true path "versions.yml", emit: versions - + [2025-11-27 15:50:36,571] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/local/clair3/main.nf [2025-11-27 15:50:36,571] nf_core.components.nfcore_component [DEBUG ] Topics: {} [2025-11-27 15:50:36,573] nf_core.components.nfcore_component [DEBUG ] Found 8 inputs in modules/nf-core/ascat/main.nf [2025-11-27 15:50:36,573] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'input_normal': {}}, {'index_normal': {}}, {'input_tumor': {}}, {'index_tumor': {}}], {'genomeVersion': {}}, {'allele_files': {}}, {'loci_files': {}}, {'bed_file': {}}, {'fasta': {}}, {'gc_file': {}}, {'rt_file': {}}] -[2025-11-27 15:50:36,573] nf_core.components.nfcore_component [DEBUG ] Found output_data: +[2025-11-27 15:50:36,573] nf_core.components.nfcore_component [DEBUG ] Found output_data: tuple val(meta), path("*alleleFrequencies_chr*.txt"), emit: allelefreqs tuple val(meta), path("*BAF.txt"), emit: bafs tuple val(meta), path("*cnvs.txt"), emit: cnvs @@ -401,10 +401,10 @@ modules.json tuple val(meta), path("*segments_raw.txt"), emit: segments_raw, optional: true path "versions.yml", emit: versions - + [2025-11-27 15:50:36,573] nf_core.components.nfcore_component [DEBUG ] Found 11 outputs in modules/nf-core/ascat/main.nf [2025-11-27 15:50:36,573] nf_core.components.nfcore_component [DEBUG ] Outputs: {'allelefreqs': [[{'meta': {}}, {'*alleleFrequencies_chr*.txt': {}}]], 'bafs': [[{'meta': {}}, {'*BAF.txt': {}}]], 'cnvs': [[{'meta': {}}, {'*cnvs.txt': {}}]], 'logrs': [[{'meta': {}}, {'*LogR.txt': {}}]], 'metrics': [[{'meta': {}}, {'*metrics.txt': {}}]], 'png': [[{'meta': {}}, {'*png': {}}]], 'pdf': [[{'meta': {}}, {'*pdf': {}}]], 'purityploidy': [[{'meta': {}}, {'*purityploidy.txt': {}}]], 'segments': [[{'meta': {}}, {'*segments.txt': {}}]], 'segments_raw': [[{'meta': {}}, {'*segments_raw.txt': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:50:36,573] nf_core.components.nfcore_component [DEBUG ] Output data: +[2025-11-27 15:50:36,573] nf_core.components.nfcore_component [DEBUG ] Output data: tuple val(meta), path("*alleleFrequencies_chr*.txt"), emit: allelefreqs tuple val(meta), path("*BAF.txt"), emit: bafs tuple val(meta), path("*cnvs.txt"), emit: cnvs @@ -417,7 +417,7 @@ modules.json tuple val(meta), path("*segments_raw.txt"), emit: segments_raw, optional: true path "versions.yml", emit: versions - + [2025-11-27 15:50:36,573] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/ascat/main.nf [2025-11-27 15:50:36,573] nf_core.components.nfcore_component [DEBUG ] Topics: {} [2025-11-27 15:50:36,574] git.util [DEBUG ] sys.platform='linux', git_executable='git' @@ -434,22 +434,22 @@ modules.json [2025-11-27 15:50:37,056] nf_core.components.components_differ [DEBUG ] Applying patch to modules/nf-core/ascat/main.nf [2025-11-27 15:50:37,056] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/nf-core/bcftools/concat/main.nf [2025-11-27 15:50:37,057] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'vcfs': {}}, {'tbi': {}}]] -[2025-11-27 15:50:37,057] nf_core.components.nfcore_component [DEBUG ] Found output_data: +[2025-11-27 15:50:37,057] nf_core.components.nfcore_component [DEBUG ] Found output_data: tuple val(meta), path("${prefix}.${extension}") , emit: vcf tuple val(meta), path("${prefix}.${extension}.tbi"), emit: tbi, optional: true tuple val(meta), path("${prefix}.${extension}.csi"), emit: csi, optional: true path "versions.yml" , emit: versions - + [2025-11-27 15:50:37,057] nf_core.components.nfcore_component [DEBUG ] Found 4 outputs in modules/nf-core/bcftools/concat/main.nf [2025-11-27 15:50:37,057] nf_core.components.nfcore_component [DEBUG ] Outputs: {'vcf': [[{'meta': {}}, {'${prefix}.${extension}': {}}]], 'tbi': [[{'meta': {}}, {'${prefix}.${extension}.tbi': {}}]], 'csi': [[{'meta': {}}, {'${prefix}.${extension}.csi': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:50:37,057] nf_core.components.nfcore_component [DEBUG ] Output data: +[2025-11-27 15:50:37,057] nf_core.components.nfcore_component [DEBUG ] Output data: tuple val(meta), path("${prefix}.${extension}") , emit: vcf tuple val(meta), path("${prefix}.${extension}.tbi"), emit: tbi, optional: true tuple val(meta), path("${prefix}.${extension}.csi"), emit: csi, optional: true path "versions.yml" , emit: versions - + [2025-11-27 15:50:37,057] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/bcftools/concat/main.nf [2025-11-27 15:50:37,057] nf_core.components.nfcore_component [DEBUG ] Topics: {} [2025-11-27 15:50:37,057] git.util [DEBUG ] sys.platform='linux', git_executable='git' @@ -473,20 +473,20 @@ modules.json [2025-11-27 15:50:38,018] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) [2025-11-27 15:50:38,212] nf_core.components.nfcore_component [DEBUG ] Found 4 inputs in modules/nf-core/bcftools/merge/main.nf [2025-11-27 15:50:38,212] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'vcfs': {}}, {'tbis': {}}], [{'meta2': {}}, {'fasta': {}}], [{'meta3': {}}, {'fai': {}}], [{'meta4': {}}, {'bed': {}}]] -[2025-11-27 15:50:38,212] nf_core.components.nfcore_component [DEBUG ] Found output_data: +[2025-11-27 15:50:38,212] nf_core.components.nfcore_component [DEBUG ] Found output_data: tuple val(meta), path("*.{bcf,vcf}{,.gz}"), emit: vcf tuple val(meta), path("*.{csi,tbi}") , emit: index, optional: true path "versions.yml" , emit: versions - + [2025-11-27 15:50:38,212] nf_core.components.nfcore_component [DEBUG ] Found 3 outputs in modules/nf-core/bcftools/merge/main.nf [2025-11-27 15:50:38,213] nf_core.components.nfcore_component [DEBUG ] Outputs: {'vcf': [[{'meta': {}}, {'*.{bcf,vcf}{,.gz}': {}}]], 'index': [[{'meta': {}}, {'*.{csi,tbi}': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:50:38,213] nf_core.components.nfcore_component [DEBUG ] Output data: +[2025-11-27 15:50:38,213] nf_core.components.nfcore_component [DEBUG ] Output data: tuple val(meta), path("*.{bcf,vcf}{,.gz}"), emit: vcf tuple val(meta), path("*.{csi,tbi}") , emit: index, optional: true path "versions.yml" , emit: versions - + [2025-11-27 15:50:38,213] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/bcftools/merge/main.nf [2025-11-27 15:50:38,213] nf_core.components.nfcore_component [DEBUG ] Topics: {} [2025-11-27 15:50:38,213] git.util [DEBUG ] sys.platform='linux', git_executable='git' @@ -510,22 +510,22 @@ modules.json [2025-11-27 15:50:42,382] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) [2025-11-27 15:50:45,573] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/nf-core/bcftools/sort/main.nf [2025-11-27 15:50:45,573] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'vcf': {}}]] -[2025-11-27 15:50:45,573] nf_core.components.nfcore_component [DEBUG ] Found output_data: +[2025-11-27 15:50:45,573] nf_core.components.nfcore_component [DEBUG ] Found output_data: tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf tuple val(meta), path("*.tbi") , emit: tbi, optional: true tuple val(meta), path("*.csi") , emit: csi, optional: true path "versions.yml" , emit: versions - + [2025-11-27 15:50:45,573] nf_core.components.nfcore_component [DEBUG ] Found 4 outputs in modules/nf-core/bcftools/sort/main.nf [2025-11-27 15:50:45,573] nf_core.components.nfcore_component [DEBUG ] Outputs: {'vcf': [[{'meta': {}}, {'*.{vcf,vcf.gz,bcf,bcf.gz}': {}}]], 'tbi': [[{'meta': {}}, {'*.tbi': {}}]], 'csi': [[{'meta': {}}, {'*.csi': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:50:45,573] nf_core.components.nfcore_component [DEBUG ] Output data: +[2025-11-27 15:50:45,573] nf_core.components.nfcore_component [DEBUG ] Output data: tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf tuple val(meta), path("*.tbi") , emit: tbi, optional: true tuple val(meta), path("*.csi") , emit: csi, optional: true path "versions.yml" , emit: versions - + [2025-11-27 15:50:45,573] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/bcftools/sort/main.nf [2025-11-27 15:50:45,573] nf_core.components.nfcore_component [DEBUG ] Topics: {} [2025-11-27 15:50:45,573] git.util [DEBUG ] sys.platform='linux', git_executable='git' @@ -542,18 +542,18 @@ modules.json [2025-11-27 15:50:46,043] nf_core.components.components_differ [DEBUG ] Applying patch to modules/nf-core/bcftools/sort/main.nf [2025-11-27 15:50:46,044] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/nf-core/ensemblvep/download/main.nf [2025-11-27 15:50:46,044] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'assembly': {}}, {'species': {}}, {'cache_version': {}}]] -[2025-11-27 15:50:46,044] nf_core.components.nfcore_component [DEBUG ] Found output_data: +[2025-11-27 15:50:46,044] nf_core.components.nfcore_component [DEBUG ] Found output_data: tuple val(meta), path(prefix), emit: cache path "versions.yml", emit: versions - + [2025-11-27 15:50:46,044] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/nf-core/ensemblvep/download/main.nf [2025-11-27 15:50:46,044] nf_core.components.nfcore_component [DEBUG ] Outputs: {'cache': [[{'meta': {}}, {'prefix': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:50:46,044] nf_core.components.nfcore_component [DEBUG ] Output data: +[2025-11-27 15:50:46,044] nf_core.components.nfcore_component [DEBUG ] Output data: tuple val(meta), path(prefix), emit: cache path "versions.yml", emit: versions - + [2025-11-27 15:50:46,044] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/ensemblvep/download/main.nf [2025-11-27 15:50:46,044] nf_core.components.nfcore_component [DEBUG ] Topics: {} [2025-11-27 15:50:46,044] git.util [DEBUG ] sys.platform='linux', git_executable='git' @@ -577,7 +577,7 @@ modules.json [2025-11-27 15:50:49,974] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) [2025-11-27 15:50:53,302] nf_core.components.nfcore_component [DEBUG ] Found 9 inputs in modules/nf-core/ensemblvep/vep/main.nf [2025-11-27 15:50:53,302] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'vcf': {}}, {'custom_extra_files': {}}], {'genome': {}}, {'species': {}}, {'cache_version': {}}, {'cache': {}}, [{'meta2': {}}, {'fasta': {}}], {'extra_files': {}}, {'custom_vep': {}}, {'custom_vep_tbi': {}}] -[2025-11-27 15:50:53,302] nf_core.components.nfcore_component [DEBUG ] Found output_data: +[2025-11-27 15:50:53,302] nf_core.components.nfcore_component [DEBUG ] Found output_data: tuple val(meta), path("*.vcf.gz"), emit: vcf, optional: true tuple val(meta), path("*.vcf.gz.tbi"), emit: tbi, optional: true tuple val(meta), path("*.tab.gz"), emit: tab, optional: true @@ -585,10 +585,10 @@ modules.json path "*.html", emit: report, optional: true path "versions.yml", emit: versions - + [2025-11-27 15:50:53,302] nf_core.components.nfcore_component [DEBUG ] Found 6 outputs in modules/nf-core/ensemblvep/vep/main.nf [2025-11-27 15:50:53,302] nf_core.components.nfcore_component [DEBUG ] Outputs: {'vcf': [[{'meta': {}}, {'*.vcf.gz': {}}]], 'tbi': [[{'meta': {}}, {'*.vcf.gz.tbi': {}}]], 'tab': [[{'meta': {}}, {'*.tab.gz': {}}]], 'json': [[{'meta': {}}, {'*.json.gz': {}}]], 'report': [{'*.html': {}}], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:50:53,302] nf_core.components.nfcore_component [DEBUG ] Output data: +[2025-11-27 15:50:53,302] nf_core.components.nfcore_component [DEBUG ] Output data: tuple val(meta), path("*.vcf.gz"), emit: vcf, optional: true tuple val(meta), path("*.vcf.gz.tbi"), emit: tbi, optional: true tuple val(meta), path("*.tab.gz"), emit: tab, optional: true @@ -596,7 +596,7 @@ modules.json path "*.html", emit: report, optional: true path "versions.yml", emit: versions - + [2025-11-27 15:50:53,302] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/ensemblvep/vep/main.nf [2025-11-27 15:50:53,302] nf_core.components.nfcore_component [DEBUG ] Topics: {} [2025-11-27 15:50:53,302] git.util [DEBUG ] sys.platform='linux', git_executable='git' @@ -613,20 +613,20 @@ modules.json [2025-11-27 15:50:53,709] nf_core.components.components_differ [DEBUG ] Applying patch to modules/nf-core/ensemblvep/vep/main.nf [2025-11-27 15:50:53,709] nf_core.components.nfcore_component [DEBUG ] Found 3 inputs in modules/nf-core/longphase/haplotag/main.nf [2025-11-27 15:50:53,709] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'bam': {}}, {'bai': {}}, {'snps': {}}, {'svs': {}}, {'mods': {}}], [{'meta2': {}}, {'fasta': {}}], [{'meta3': {}}, {'fai': {}}]] -[2025-11-27 15:50:53,710] nf_core.components.nfcore_component [DEBUG ] Found output_data: +[2025-11-27 15:50:53,710] nf_core.components.nfcore_component [DEBUG ] Found output_data: tuple val(meta), path("*.{bam,cram}"), emit: bam tuple val(meta), path("*.log") , emit: log , optional: true path "versions.yml" , emit: versions - + [2025-11-27 15:50:53,710] nf_core.components.nfcore_component [DEBUG ] Found 3 outputs in modules/nf-core/longphase/haplotag/main.nf [2025-11-27 15:50:53,710] nf_core.components.nfcore_component [DEBUG ] Outputs: {'bam': [[{'meta': {}}, {'*.{bam,cram}': {}}]], 'log': [[{'meta': {}}, {'*.log': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:50:53,710] nf_core.components.nfcore_component [DEBUG ] Output data: +[2025-11-27 15:50:53,710] nf_core.components.nfcore_component [DEBUG ] Output data: tuple val(meta), path("*.{bam,cram}"), emit: bam tuple val(meta), path("*.log") , emit: log , optional: true path "versions.yml" , emit: versions - + [2025-11-27 15:50:53,710] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/longphase/haplotag/main.nf [2025-11-27 15:50:53,710] nf_core.components.nfcore_component [DEBUG ] Topics: {} [2025-11-27 15:50:53,710] git.util [DEBUG ] sys.platform='linux', git_executable='git' @@ -650,20 +650,20 @@ modules.json [2025-11-27 15:50:58,312] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) [2025-11-27 15:51:02,039] nf_core.components.nfcore_component [DEBUG ] Found 3 inputs in modules/nf-core/longphase/phase/main.nf [2025-11-27 15:51:02,039] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'bam': {}}, {'bai': {}}, {'snps': {}}, {'svs': {}}, {'mods': {}}], [{'meta2': {}}, {'fasta': {}}], [{'meta3': {}}, {'fai': {}}]] -[2025-11-27 15:51:02,039] nf_core.components.nfcore_component [DEBUG ] Found output_data: +[2025-11-27 15:51:02,039] nf_core.components.nfcore_component [DEBUG ] Found output_data: tuple val(meta), path("*.vcf.gz") , emit: vcf tuple val(meta), path("*.vcf.gz.tbi") , emit: tbi path "versions.yml" , emit: versions - + [2025-11-27 15:51:02,039] nf_core.components.nfcore_component [DEBUG ] Found 3 outputs in modules/nf-core/longphase/phase/main.nf [2025-11-27 15:51:02,039] nf_core.components.nfcore_component [DEBUG ] Outputs: {'vcf': [[{'meta': {}}, {'*.vcf.gz': {}}]], 'tbi': [[{'meta': {}}, {'*.vcf.gz.tbi': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:51:02,039] nf_core.components.nfcore_component [DEBUG ] Output data: +[2025-11-27 15:51:02,039] nf_core.components.nfcore_component [DEBUG ] Output data: tuple val(meta), path("*.vcf.gz") , emit: vcf tuple val(meta), path("*.vcf.gz.tbi") , emit: tbi path "versions.yml" , emit: versions - + [2025-11-27 15:51:02,039] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/longphase/phase/main.nf [2025-11-27 15:51:02,039] nf_core.components.nfcore_component [DEBUG ] Topics: {} [2025-11-27 15:51:02,039] git.util [DEBUG ] sys.platform='linux', git_executable='git' @@ -688,22 +688,22 @@ modules.json [2025-11-27 15:51:05,703] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) [2025-11-27 15:51:09,496] nf_core.components.nfcore_component [DEBUG ] Found 6 inputs in modules/nf-core/minimap2/align/main.nf [2025-11-27 15:51:09,496] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'reads': {}}], [{'meta2': {}}, {'reference': {}}], {'bam_format': {}}, {'bam_index_extension': {}}, {'cigar_paf_format': {}}, {'cigar_bam': {}}] -[2025-11-27 15:51:09,496] nf_core.components.nfcore_component [DEBUG ] Found output_data: +[2025-11-27 15:51:09,496] nf_core.components.nfcore_component [DEBUG ] Found output_data: tuple val(meta), path("*.paf") , optional: true, emit: paf tuple val(meta), path("*.bam") , optional: true, emit: bam tuple val(meta), path("*.bam.${bam_index_extension}"), optional: true, emit: index path "versions.yml" , emit: versions - + [2025-11-27 15:51:09,496] nf_core.components.nfcore_component [DEBUG ] Found 4 outputs in modules/nf-core/minimap2/align/main.nf [2025-11-27 15:51:09,496] nf_core.components.nfcore_component [DEBUG ] Outputs: {'paf': [[{'meta': {}}, {'*.paf': {}}]], 'bam': [[{'meta': {}}, {'*.bam': {}}]], 'index': [[{'meta': {}}, {'*.bam.${bam_index_extension}': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:51:09,496] nf_core.components.nfcore_component [DEBUG ] Output data: +[2025-11-27 15:51:09,496] nf_core.components.nfcore_component [DEBUG ] Output data: tuple val(meta), path("*.paf") , optional: true, emit: paf tuple val(meta), path("*.bam") , optional: true, emit: bam tuple val(meta), path("*.bam.${bam_index_extension}"), optional: true, emit: index path "versions.yml" , emit: versions - + [2025-11-27 15:51:09,496] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/minimap2/align/main.nf [2025-11-27 15:51:09,496] nf_core.components.nfcore_component [DEBUG ] Topics: {} [2025-11-27 15:51:09,496] git.util [DEBUG ] sys.platform='linux', git_executable='git' @@ -728,18 +728,18 @@ modules.json [2025-11-27 15:51:13,177] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) [2025-11-27 15:51:16,904] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/nf-core/minimap2/index/main.nf [2025-11-27 15:51:16,904] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'fasta': {}}]] -[2025-11-27 15:51:16,904] nf_core.components.nfcore_component [DEBUG ] Found output_data: +[2025-11-27 15:51:16,904] nf_core.components.nfcore_component [DEBUG ] Found output_data: tuple val(meta), path("*.mmi"), emit: index path "versions.yml" , emit: versions - + [2025-11-27 15:51:16,904] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/nf-core/minimap2/index/main.nf [2025-11-27 15:51:16,904] nf_core.components.nfcore_component [DEBUG ] Outputs: {'index': [[{'meta': {}}, {'*.mmi': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:51:16,904] nf_core.components.nfcore_component [DEBUG ] Output data: +[2025-11-27 15:51:16,904] nf_core.components.nfcore_component [DEBUG ] Output data: tuple val(meta), path("*.mmi"), emit: index path "versions.yml" , emit: versions - + [2025-11-27 15:51:16,904] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/minimap2/index/main.nf [2025-11-27 15:51:16,904] nf_core.components.nfcore_component [DEBUG ] Topics: {} [2025-11-27 15:51:16,904] git.util [DEBUG ] sys.platform='linux', git_executable='git' @@ -763,22 +763,22 @@ modules.json [2025-11-27 15:51:20,761] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) [2025-11-27 15:51:24,622] nf_core.components.nfcore_component [DEBUG ] Found 3 inputs in modules/nf-core/modkit/pileup/main.nf [2025-11-27 15:51:24,623] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'bam': {}}, {'bai': {}}], [{'meta2': {}}, {'fasta': {}}, {'fai': {}}], [{'meta3': {}}, {'bed': {}}]] -[2025-11-27 15:51:24,623] nf_core.components.nfcore_component [DEBUG ] Found output_data: +[2025-11-27 15:51:24,623] nf_core.components.nfcore_component [DEBUG ] Found output_data: tuple val(meta), path("*.bed") , emit: bed , optional: true tuple val(meta), path("*.bedgraph"), emit: bedgraph, optional: true tuple val(meta), path("*.log") , emit: log , optional: true path "versions.yml" , emit: versions - + [2025-11-27 15:51:24,623] nf_core.components.nfcore_component [DEBUG ] Found 4 outputs in modules/nf-core/modkit/pileup/main.nf [2025-11-27 15:51:24,623] nf_core.components.nfcore_component [DEBUG ] Outputs: {'bed': [[{'meta': {}}, {'*.bed': {}}]], 'bedgraph': [[{'meta': {}}, {'*.bedgraph': {}}]], 'log': [[{'meta': {}}, {'*.log': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:51:24,623] nf_core.components.nfcore_component [DEBUG ] Output data: +[2025-11-27 15:51:24,623] nf_core.components.nfcore_component [DEBUG ] Output data: tuple val(meta), path("*.bed") , emit: bed , optional: true tuple val(meta), path("*.bedgraph"), emit: bedgraph, optional: true tuple val(meta), path("*.log") , emit: log , optional: true path "versions.yml" , emit: versions - + [2025-11-27 15:51:24,623] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/modkit/pileup/main.nf [2025-11-27 15:51:24,623] nf_core.components.nfcore_component [DEBUG ] Topics: {} [2025-11-27 15:51:24,623] git.util [DEBUG ] sys.platform='linux', git_executable='git' @@ -802,7 +802,7 @@ modules.json [2025-11-27 15:51:28,381] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) [2025-11-27 15:51:32,189] nf_core.components.nfcore_component [DEBUG ] Found 2 inputs in modules/nf-core/mosdepth/main.nf [2025-11-27 15:51:32,189] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'bam': {}}, {'bai': {}}, {'bed': {}}], [{'meta2': {}}, {'fasta': {}}]] -[2025-11-27 15:51:32,189] nf_core.components.nfcore_component [DEBUG ] Found output_data: +[2025-11-27 15:51:32,189] nf_core.components.nfcore_component [DEBUG ] Found output_data: tuple val(meta), path('*.global.dist.txt') , emit: global_txt tuple val(meta), path('*.summary.txt') , emit: summary_txt tuple val(meta), path('*.region.dist.txt') , optional:true, emit: regions_txt @@ -817,10 +817,10 @@ modules.json tuple val(meta), path('*.thresholds.bed.gz.csi'), optional:true, emit: thresholds_csi path "versions.yml" , emit: versions - + [2025-11-27 15:51:32,190] nf_core.components.nfcore_component [DEBUG ] Found 13 outputs in modules/nf-core/mosdepth/main.nf [2025-11-27 15:51:32,190] nf_core.components.nfcore_component [DEBUG ] Outputs: {'global_txt': [[{'meta': {}}, {'*.global.dist.txt': {}}]], 'summary_txt': [[{'meta': {}}, {'*.summary.txt': {}}]], 'regions_txt': [[{'meta': {}}, {'*.region.dist.txt': {}}]], 'per_base_d4': [[{'meta': {}}, {'*.per-base.d4': {}}]], 'per_base_bed': [[{'meta': {}}, {'*.per-base.bed.gz': {}}]], 'per_base_csi': [[{'meta': {}}, {'*.per-base.bed.gz.csi': {}}]], 'regions_bed': [[{'meta': {}}, {'*.regions.bed.gz': {}}]], 'regions_csi': [[{'meta': {}}, {'*.regions.bed.gz.csi': {}}]], 'quantized_bed': [[{'meta': {}}, {'*.quantized.bed.gz': {}}]], 'quantized_csi': [[{'meta': {}}, {'*.quantized.bed.gz.csi': {}}]], 'thresholds_bed': [[{'meta': {}}, {'*.thresholds.bed.gz': {}}]], 'thresholds_csi': [[{'meta': {}}, {'*.thresholds.bed.gz.csi': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:51:32,190] nf_core.components.nfcore_component [DEBUG ] Output data: +[2025-11-27 15:51:32,190] nf_core.components.nfcore_component [DEBUG ] Output data: tuple val(meta), path('*.global.dist.txt') , emit: global_txt tuple val(meta), path('*.summary.txt') , emit: summary_txt tuple val(meta), path('*.region.dist.txt') , optional:true, emit: regions_txt @@ -835,7 +835,7 @@ modules.json tuple val(meta), path('*.thresholds.bed.gz.csi'), optional:true, emit: thresholds_csi path "versions.yml" , emit: versions - + [2025-11-27 15:51:32,190] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/mosdepth/main.nf [2025-11-27 15:51:32,190] nf_core.components.nfcore_component [DEBUG ] Topics: {} [2025-11-27 15:51:32,190] git.util [DEBUG ] sys.platform='linux', git_executable='git' @@ -859,22 +859,22 @@ modules.json [2025-11-27 15:51:35,682] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) [2025-11-27 15:51:39,445] nf_core.components.nfcore_component [DEBUG ] Found 6 inputs in modules/nf-core/multiqc/main.nf [2025-11-27 15:51:39,445] nf_core.components.nfcore_component [DEBUG ] Inputs: [{'multiqc_files': {}}, {'multiqc_config': {}}, {'extra_multiqc_config': {}}, {'multiqc_logo': {}}, {'replace_names': {}}, {'sample_names': {}}] -[2025-11-27 15:51:39,445] nf_core.components.nfcore_component [DEBUG ] Found output_data: +[2025-11-27 15:51:39,445] nf_core.components.nfcore_component [DEBUG ] Found output_data: path "*multiqc_report.html", emit: report path "*_data" , emit: data path "*_plots" , optional:true, emit: plots path "versions.yml" , emit: versions - + [2025-11-27 15:51:39,445] nf_core.components.nfcore_component [DEBUG ] Found 4 outputs in modules/nf-core/multiqc/main.nf [2025-11-27 15:51:39,445] nf_core.components.nfcore_component [DEBUG ] Outputs: {'report': [{'*multiqc_report.html': {}}], 'data': [{'*_data': {}}], 'plots': [{'*_plots': {}}], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:51:39,445] nf_core.components.nfcore_component [DEBUG ] Output data: +[2025-11-27 15:51:39,445] nf_core.components.nfcore_component [DEBUG ] Output data: path "*multiqc_report.html", emit: report path "*_data" , emit: data path "*_plots" , optional:true, emit: plots path "versions.yml" , emit: versions - + [2025-11-27 15:51:39,445] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/multiqc/main.nf [2025-11-27 15:51:39,445] nf_core.components.nfcore_component [DEBUG ] Topics: {} [2025-11-27 15:51:39,445] git.util [DEBUG ] sys.platform='linux', git_executable='git' @@ -898,18 +898,18 @@ modules.json [2025-11-27 15:51:43,079] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) [2025-11-27 15:51:46,118] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/nf-core/pigz/uncompress/main.nf [2025-11-27 15:51:46,119] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'zip': {}}]] -[2025-11-27 15:51:46,119] nf_core.components.nfcore_component [DEBUG ] Found output_data: +[2025-11-27 15:51:46,119] nf_core.components.nfcore_component [DEBUG ] Found output_data: tuple val(meta), path("${uncompressed_filename}") , emit: file path "versions.yml" , emit: versions - + [2025-11-27 15:51:46,119] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/nf-core/pigz/uncompress/main.nf [2025-11-27 15:51:46,119] nf_core.components.nfcore_component [DEBUG ] Outputs: {'file': [[{'meta': {}}, {'${uncompressed_filename}': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:51:46,119] nf_core.components.nfcore_component [DEBUG ] Output data: +[2025-11-27 15:51:46,119] nf_core.components.nfcore_component [DEBUG ] Output data: tuple val(meta), path("${uncompressed_filename}") , emit: file path "versions.yml" , emit: versions - + [2025-11-27 15:51:46,119] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/pigz/uncompress/main.nf [2025-11-27 15:51:46,119] nf_core.components.nfcore_component [DEBUG ] Topics: {} [2025-11-27 15:51:46,119] git.util [DEBUG ] sys.platform='linux', git_executable='git' @@ -933,22 +933,22 @@ modules.json [2025-11-27 15:51:49,638] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) [2025-11-27 15:51:53,446] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/nf-core/samtools/cat/main.nf [2025-11-27 15:51:53,446] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'input_files': {}}]] -[2025-11-27 15:51:53,446] nf_core.components.nfcore_component [DEBUG ] Found output_data: +[2025-11-27 15:51:53,446] nf_core.components.nfcore_component [DEBUG ] Found output_data: tuple val(meta), path("${prefix}.bam") , optional:true, emit: bam tuple val(meta), path("${prefix}.cram"), optional:true, emit: cram path "versions.yml" , emit: versions - + [2025-11-27 15:51:53,446] nf_core.components.nfcore_component [DEBUG ] Found 3 outputs in modules/nf-core/samtools/cat/main.nf [2025-11-27 15:51:53,446] nf_core.components.nfcore_component [DEBUG ] Outputs: {'bam': [[{'meta': {}}, {'${prefix}.bam': {}}]], 'cram': [[{'meta': {}}, {'${prefix}.cram': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:51:53,446] nf_core.components.nfcore_component [DEBUG ] Output data: +[2025-11-27 15:51:53,446] nf_core.components.nfcore_component [DEBUG ] Output data: tuple val(meta), path("${prefix}.bam") , optional:true, emit: bam tuple val(meta), path("${prefix}.cram"), optional:true, emit: cram path "versions.yml" , emit: versions - + [2025-11-27 15:51:53,446] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/samtools/cat/main.nf [2025-11-27 15:51:53,446] nf_core.components.nfcore_component [DEBUG ] Topics: {} [2025-11-27 15:51:53,446] git.util [DEBUG ] sys.platform='linux', git_executable='git' @@ -972,24 +972,24 @@ modules.json [2025-11-27 15:51:57,097] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) [2025-11-27 15:52:00,645] nf_core.components.nfcore_component [DEBUG ] Found 3 inputs in modules/nf-core/samtools/faidx/main.nf [2025-11-27 15:52:00,645] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'fasta': {}}], [{'meta2': {}}, {'fai': {}}], {'get_sizes': {}}] -[2025-11-27 15:52:00,645] nf_core.components.nfcore_component [DEBUG ] Found output_data: +[2025-11-27 15:52:00,645] nf_core.components.nfcore_component [DEBUG ] Found output_data: tuple val(meta), path ("*.{fa,fasta}") , emit: fa, optional: true tuple val(meta), path ("*.sizes") , emit: sizes, optional: true tuple val(meta), path ("*.fai") , emit: fai, optional: true tuple val(meta), path ("*.gzi") , emit: gzi, optional: true path "versions.yml" , emit: versions - + [2025-11-27 15:52:00,645] nf_core.components.nfcore_component [DEBUG ] Found 5 outputs in modules/nf-core/samtools/faidx/main.nf [2025-11-27 15:52:00,645] nf_core.components.nfcore_component [DEBUG ] Outputs: {'fa': [[{'meta': {}}, {'*.{fa,fasta}': {}}]], 'sizes': [[{'meta': {}}, {'*.sizes': {}}]], 'fai': [[{'meta': {}}, {'*.fai': {}}]], 'gzi': [[{'meta': {}}, {'*.gzi': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:52:00,645] nf_core.components.nfcore_component [DEBUG ] Output data: +[2025-11-27 15:52:00,645] nf_core.components.nfcore_component [DEBUG ] Output data: tuple val(meta), path ("*.{fa,fasta}") , emit: fa, optional: true tuple val(meta), path ("*.sizes") , emit: sizes, optional: true tuple val(meta), path ("*.fai") , emit: fai, optional: true tuple val(meta), path ("*.gzi") , emit: gzi, optional: true path "versions.yml" , emit: versions - + [2025-11-27 15:52:00,645] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/samtools/faidx/main.nf [2025-11-27 15:52:00,645] nf_core.components.nfcore_component [DEBUG ] Topics: {} [2025-11-27 15:52:00,645] git.util [DEBUG ] sys.platform='linux', git_executable='git' @@ -1013,18 +1013,18 @@ modules.json [2025-11-27 15:52:04,805] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) [2025-11-27 15:52:08,779] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/nf-core/samtools/flagstat/main.nf [2025-11-27 15:52:08,779] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'bam': {}}, {'bai': {}}]] -[2025-11-27 15:52:08,779] nf_core.components.nfcore_component [DEBUG ] Found output_data: +[2025-11-27 15:52:08,779] nf_core.components.nfcore_component [DEBUG ] Found output_data: tuple val(meta), path("*.flagstat"), emit: flagstat path "versions.yml" , emit: versions - + [2025-11-27 15:52:08,779] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/nf-core/samtools/flagstat/main.nf [2025-11-27 15:52:08,779] nf_core.components.nfcore_component [DEBUG ] Outputs: {'flagstat': [[{'meta': {}}, {'*.flagstat': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:52:08,779] nf_core.components.nfcore_component [DEBUG ] Output data: +[2025-11-27 15:52:08,779] nf_core.components.nfcore_component [DEBUG ] Output data: tuple val(meta), path("*.flagstat"), emit: flagstat path "versions.yml" , emit: versions - + [2025-11-27 15:52:08,779] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/samtools/flagstat/main.nf [2025-11-27 15:52:08,779] nf_core.components.nfcore_component [DEBUG ] Topics: {} [2025-11-27 15:52:08,779] git.util [DEBUG ] sys.platform='linux', git_executable='git' @@ -1048,18 +1048,18 @@ modules.json [2025-11-27 15:52:12,547] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) [2025-11-27 15:52:16,622] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/nf-core/samtools/idxstats/main.nf [2025-11-27 15:52:16,622] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'bam': {}}, {'bai': {}}]] -[2025-11-27 15:52:16,622] nf_core.components.nfcore_component [DEBUG ] Found output_data: +[2025-11-27 15:52:16,622] nf_core.components.nfcore_component [DEBUG ] Found output_data: tuple val(meta), path("*.idxstats"), emit: idxstats path "versions.yml" , emit: versions - + [2025-11-27 15:52:16,623] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/nf-core/samtools/idxstats/main.nf [2025-11-27 15:52:16,623] nf_core.components.nfcore_component [DEBUG ] Outputs: {'idxstats': [[{'meta': {}}, {'*.idxstats': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:52:16,623] nf_core.components.nfcore_component [DEBUG ] Output data: +[2025-11-27 15:52:16,623] nf_core.components.nfcore_component [DEBUG ] Output data: tuple val(meta), path("*.idxstats"), emit: idxstats path "versions.yml" , emit: versions - + [2025-11-27 15:52:16,623] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/samtools/idxstats/main.nf [2025-11-27 15:52:16,623] nf_core.components.nfcore_component [DEBUG ] Topics: {} [2025-11-27 15:52:16,623] git.util [DEBUG ] sys.platform='linux', git_executable='git' @@ -1083,22 +1083,22 @@ modules.json [2025-11-27 15:52:20,320] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) [2025-11-27 15:52:23,973] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/nf-core/samtools/index/main.nf [2025-11-27 15:52:23,973] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'input': {}}]] -[2025-11-27 15:52:23,973] nf_core.components.nfcore_component [DEBUG ] Found output_data: +[2025-11-27 15:52:23,973] nf_core.components.nfcore_component [DEBUG ] Found output_data: tuple val(meta), path("*.bai") , optional:true, emit: bai tuple val(meta), path("*.csi") , optional:true, emit: csi tuple val(meta), path("*.crai"), optional:true, emit: crai path "versions.yml" , emit: versions - + [2025-11-27 15:52:23,973] nf_core.components.nfcore_component [DEBUG ] Found 4 outputs in modules/nf-core/samtools/index/main.nf [2025-11-27 15:52:23,973] nf_core.components.nfcore_component [DEBUG ] Outputs: {'bai': [[{'meta': {}}, {'*.bai': {}}]], 'csi': [[{'meta': {}}, {'*.csi': {}}]], 'crai': [[{'meta': {}}, {'*.crai': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:52:23,973] nf_core.components.nfcore_component [DEBUG ] Output data: +[2025-11-27 15:52:23,973] nf_core.components.nfcore_component [DEBUG ] Output data: tuple val(meta), path("*.bai") , optional:true, emit: bai tuple val(meta), path("*.csi") , optional:true, emit: csi tuple val(meta), path("*.crai"), optional:true, emit: crai path "versions.yml" , emit: versions - + [2025-11-27 15:52:23,974] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/samtools/index/main.nf [2025-11-27 15:52:23,974] nf_core.components.nfcore_component [DEBUG ] Topics: {} [2025-11-27 15:52:23,974] git.util [DEBUG ] sys.platform='linux', git_executable='git' @@ -1122,18 +1122,18 @@ modules.json [2025-11-27 15:52:27,563] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) [2025-11-27 15:52:31,361] nf_core.components.nfcore_component [DEBUG ] Found 2 inputs in modules/nf-core/samtools/stats/main.nf [2025-11-27 15:52:31,361] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'input': {}}, {'input_index': {}}], [{'meta2': {}}, {'fasta': {}}]] -[2025-11-27 15:52:31,361] nf_core.components.nfcore_component [DEBUG ] Found output_data: +[2025-11-27 15:52:31,361] nf_core.components.nfcore_component [DEBUG ] Found output_data: tuple val(meta), path("*.stats"), emit: stats path "versions.yml" , emit: versions - + [2025-11-27 15:52:31,361] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/nf-core/samtools/stats/main.nf [2025-11-27 15:52:31,361] nf_core.components.nfcore_component [DEBUG ] Outputs: {'stats': [[{'meta': {}}, {'*.stats': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:52:31,361] nf_core.components.nfcore_component [DEBUG ] Output data: +[2025-11-27 15:52:31,361] nf_core.components.nfcore_component [DEBUG ] Output data: tuple val(meta), path("*.stats"), emit: stats path "versions.yml" , emit: versions - + [2025-11-27 15:52:31,361] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/samtools/stats/main.nf [2025-11-27 15:52:31,361] nf_core.components.nfcore_component [DEBUG ] Topics: {} [2025-11-27 15:52:31,361] git.util [DEBUG ] sys.platform='linux', git_executable='git' @@ -1158,7 +1158,7 @@ modules.json [2025-11-27 15:52:34,930] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) [2025-11-27 15:52:38,673] nf_core.components.nfcore_component [DEBUG ] Found 2 inputs in modules/nf-core/severus/main.nf [2025-11-27 15:52:38,673] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'target_input': {}}, {'target_index': {}}, {'control_input': {}}, {'control_index': {}}, {'vcf': {}}, {'tbi': {}}], [{'meta2': {}}, {'bed': {}}, {'pon_path': {}}]] -[2025-11-27 15:52:38,673] nf_core.components.nfcore_component [DEBUG ] Found output_data: +[2025-11-27 15:52:38,673] nf_core.components.nfcore_component [DEBUG ] Found output_data: tuple val(meta), path("severus.log") , emit: log tuple val(meta), path("read_qual.txt") , emit: read_qual tuple val(meta), path("breakpoints_double.csv") , emit: breakpoints_double @@ -1178,10 +1178,10 @@ modules.json tuple val(meta), path("somatic_SVs/plots/severus_*.html") , emit: somatic_plots , optional: true path "versions.yml" , emit: versions - + [2025-11-27 15:52:38,673] nf_core.components.nfcore_component [DEBUG ] Found 18 outputs in modules/nf-core/severus/main.nf [2025-11-27 15:52:38,673] nf_core.components.nfcore_component [DEBUG ] Outputs: {'log': [[{'meta': {}}, {'severus.log': {}}]], 'read_qual': [[{'meta': {}}, {'read_qual.txt': {}}]], 'breakpoints_double': [[{'meta': {}}, {'breakpoints_double.csv': {}}]], 'read_alignments': [[{'meta': {}}, {'read_alignments': {}}]], 'read_ids': [[{'meta': {}}, {'read_ids.csv': {}}]], 'collapsed_dup': [[{'meta': {}}, {'severus_collaped_dup.bed': {}}]], 'loh': [[{'meta': {}}, {'severus_LOH.bed': {}}]], 'all_vcf': [[{'meta': {}}, {'all_SVs/severus_all.vcf.gz': {}}]], 'all_tbi': [[{'meta': {}}, {'all_SVs/severus_all.vcf.gz.tbi': {}}]], 'all_breakpoints_clusters_list': [[{'meta': {}}, {'all_SVs/breakpoint_clusters_list.tsv': {}}]], 'all_breakpoints_clusters': [[{'meta': {}}, {'all_SVs/breakpoint_clusters.tsv': {}}]], 'all_plots': [[{'meta': {}}, {'all_SVs/plots/severus_*.html': {}}]], 'somatic_vcf': [[{'meta': {}}, {'somatic_SVs/severus_somatic.vcf.gz': {}}]], 'somatic_tbi': [[{'meta': {}}, {'somatic_SVs/severus_somatic.vcf.gz.tbi': {}}]], 'somatic_breakpoints_clusters_list': [[{'meta': {}}, {'somatic_SVs/breakpoint_clusters_list.tsv': {}}]], 'somatic_breakpoints_clusters': [[{'meta': {}}, {'somatic_SVs/breakpoint_clusters.tsv': {}}]], 'somatic_plots': [[{'meta': {}}, {'somatic_SVs/plots/severus_*.html': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:52:38,673] nf_core.components.nfcore_component [DEBUG ] Output data: +[2025-11-27 15:52:38,673] nf_core.components.nfcore_component [DEBUG ] Output data: tuple val(meta), path("severus.log") , emit: log tuple val(meta), path("read_qual.txt") , emit: read_qual tuple val(meta), path("breakpoints_double.csv") , emit: breakpoints_double @@ -1201,7 +1201,7 @@ modules.json tuple val(meta), path("somatic_SVs/plots/severus_*.html") , emit: somatic_plots , optional: true path "versions.yml" , emit: versions - + [2025-11-27 15:52:38,673] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/severus/main.nf [2025-11-27 15:52:38,673] nf_core.components.nfcore_component [DEBUG ] Topics: {} [2025-11-27 15:52:38,674] git.util [DEBUG ] sys.platform='linux', git_executable='git' @@ -1226,18 +1226,18 @@ modules.json [2025-11-27 15:52:49,232] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) [2025-11-27 15:52:57,844] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/nf-core/untar/main.nf [2025-11-27 15:52:57,844] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'archive': {}}]] -[2025-11-27 15:52:57,844] nf_core.components.nfcore_component [DEBUG ] Found output_data: +[2025-11-27 15:52:57,844] nf_core.components.nfcore_component [DEBUG ] Found output_data: tuple val(meta), path("${prefix}"), emit: untar path "versions.yml", emit: versions - + [2025-11-27 15:52:57,844] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/nf-core/untar/main.nf [2025-11-27 15:52:57,844] nf_core.components.nfcore_component [DEBUG ] Outputs: {'untar': [[{'meta': {}}, {'${prefix}': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:52:57,844] nf_core.components.nfcore_component [DEBUG ] Output data: +[2025-11-27 15:52:57,844] nf_core.components.nfcore_component [DEBUG ] Output data: tuple val(meta), path("${prefix}"), emit: untar path "versions.yml", emit: versions - + [2025-11-27 15:52:57,844] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/untar/main.nf [2025-11-27 15:52:57,844] nf_core.components.nfcore_component [DEBUG ] Topics: {} [2025-11-27 15:52:57,845] git.util [DEBUG ] sys.platform='linux', git_executable='git' @@ -1261,18 +1261,18 @@ modules.json [2025-11-27 15:53:01,667] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) [2025-11-27 15:53:05,409] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/nf-core/unzip/main.nf [2025-11-27 15:53:05,409] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'archive': {}}]] -[2025-11-27 15:53:05,409] nf_core.components.nfcore_component [DEBUG ] Found output_data: +[2025-11-27 15:53:05,409] nf_core.components.nfcore_component [DEBUG ] Found output_data: tuple val(meta), path("${prefix}/"), emit: unzipped_archive path "versions.yml" , emit: versions - + [2025-11-27 15:53:05,409] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/nf-core/unzip/main.nf [2025-11-27 15:53:05,409] nf_core.components.nfcore_component [DEBUG ] Outputs: {'unzipped_archive': [[{'meta': {}}, {'${prefix}/': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:53:05,410] nf_core.components.nfcore_component [DEBUG ] Output data: +[2025-11-27 15:53:05,410] nf_core.components.nfcore_component [DEBUG ] Output data: tuple val(meta), path("${prefix}/"), emit: unzipped_archive path "versions.yml" , emit: versions - + [2025-11-27 15:53:05,410] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/unzip/main.nf [2025-11-27 15:53:05,410] nf_core.components.nfcore_component [DEBUG ] Topics: {} [2025-11-27 15:53:05,410] git.util [DEBUG ] sys.platform='linux', git_executable='git' @@ -1296,18 +1296,18 @@ modules.json [2025-11-27 15:53:09,447] git.cmd [DEBUG ] Popen(['git', 'checkout', 'master'], cwd=/user/leuven/351/vsc35115/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) [2025-11-27 15:53:13,327] nf_core.components.nfcore_component [DEBUG ] Found 1 inputs in modules/nf-core/wget/main.nf [2025-11-27 15:53:13,327] nf_core.components.nfcore_component [DEBUG ] Inputs: [[{'meta': {}}, {'url': {}}]] -[2025-11-27 15:53:13,327] nf_core.components.nfcore_component [DEBUG ] Found output_data: +[2025-11-27 15:53:13,327] nf_core.components.nfcore_component [DEBUG ] Found output_data: tuple val(meta), path("${prefix}.${suffix}"), emit: outfile path "versions.yml" , emit: versions - + [2025-11-27 15:53:13,327] nf_core.components.nfcore_component [DEBUG ] Found 2 outputs in modules/nf-core/wget/main.nf [2025-11-27 15:53:13,327] nf_core.components.nfcore_component [DEBUG ] Outputs: {'outfile': [[{'meta': {}}, {'${prefix}.${suffix}': {}}]], 'versions': [{'versions.yml': {}}]} -[2025-11-27 15:53:13,328] nf_core.components.nfcore_component [DEBUG ] Output data: +[2025-11-27 15:53:13,328] nf_core.components.nfcore_component [DEBUG ] Output data: tuple val(meta), path("${prefix}.${suffix}"), emit: outfile path "versions.yml" , emit: versions - + [2025-11-27 15:53:13,328] nf_core.components.nfcore_component [DEBUG ] Found 0 topics in modules/nf-core/wget/main.nf [2025-11-27 15:53:13,328] nf_core.components.nfcore_component [DEBUG ] Topics: {} [2025-11-27 15:53:13,328] git.util [DEBUG ] sys.platform='linux', git_executable='git' From 8881a18ca06648e3c183b891f61e2ca7bffeddd6 Mon Sep 17 00:00:00 2001 From: ljwharbers Date: Thu, 27 Nov 2025 16:16:33 +0100 Subject: [PATCH 39/42] whitespace --- subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf | 2 -- 1 file changed, 2 deletions(-) diff --git a/subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf b/subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf index 787e9f29..a58dc77d 100644 --- a/subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf @@ -100,8 +100,6 @@ workflow PIPELINE_INITIALISATION { } .set { ch_samplesheet } - - // ch_samplesheet -> meta: [id, paired_data, platform, sex, type] // bam: unaligned bams From 2e2f4f33c506b8f80f08357afa97a87ebb6a2937 Mon Sep 17 00:00:00 2001 From: ljwharbers Date: Thu, 27 Nov 2025 16:19:15 +0100 Subject: [PATCH 40/42] formatting --- subworkflows/local/tumor_normal_happhase.nf | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/subworkflows/local/tumor_normal_happhase.nf b/subworkflows/local/tumor_normal_happhase.nf index 923c22a5..91c7014c 100644 --- a/subworkflows/local/tumor_normal_happhase.nf +++ b/subworkflows/local/tumor_normal_happhase.nf @@ -30,7 +30,6 @@ workflow TUMOR_NORMAL_HAPPHASE { } .set{ mixed_bams } - // Get normal bams and add platform/model info for Clair3 usage // remove type from so that information can be merged easier later @@ -41,7 +40,6 @@ workflow TUMOR_NORMAL_HAPPHASE { } .set{downloaded_model_files} - mixed_bams.normal .map{ meta, bam, bai -> def basecall_model = (!meta.clair3_model || meta.clair3_model.toString().trim() in ['', '[]']) ? meta.basecall_model : meta.clair3_model @@ -56,7 +54,6 @@ workflow TUMOR_NORMAL_HAPPHASE { } .set { normal_bams_model } - normal_bams_model .combine(downloaded_model_files,by:0) .map{ basecall_model, meta, bam, bai, meta2, model -> @@ -115,7 +112,6 @@ workflow TUMOR_NORMAL_HAPPHASE { } .set{ normal_bams_germlinevcf } - // normal_bams -> meta: [id, paired_data, platform, sex, type, fiber, basecall_model] // bam: list of concatenated aligned bams // bai: indexes for bam files @@ -130,7 +126,6 @@ workflow TUMOR_NORMAL_HAPPHASE { } .set { germline_vep } - // // MODULE: LONGPHASE_PHASE // @@ -271,7 +266,6 @@ workflow TUMOR_NORMAL_HAPPHASE { // MODULE: CLAIRS // - CLAIRS ( clairs_input, fasta, @@ -282,12 +276,20 @@ workflow TUMOR_NORMAL_HAPPHASE { .join(CLAIRS.out.tbi) .set{clairs_out} + // + // MODULE: BCFTOOLS_CONCAT + // + BCFTOOLS_CONCAT( clairs_out ) ch_versions = ch_versions.mix(BCFTOOLS_CONCAT.out.versions) + // + // MODULE: BCFTOOLS_SORT + // + BCFTOOLS_SORT( BCFTOOLS_CONCAT.out.vcf ) From d841fd15bb1728781d53b2a273ca0ef9b83d1df8 Mon Sep 17 00:00:00 2001 From: ljwharbers Date: Thu, 27 Nov 2025 16:19:36 +0100 Subject: [PATCH 41/42] formatting --- subworkflows/local/tumor_only_happhase.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/tumor_only_happhase.nf b/subworkflows/local/tumor_only_happhase.nf index dd3d074b..220a8710 100644 --- a/subworkflows/local/tumor_only_happhase.nf +++ b/subworkflows/local/tumor_only_happhase.nf @@ -22,6 +22,7 @@ workflow TUMOR_ONLY_HAPPHASE { tumor_only_severus = Channel.empty() somatic_vep = Channel.empty() germline_vep = Channel.empty() + tumor_bams .map{ meta, bam, bai -> def clairSTO_model = (!meta.clairSTO_model || meta.clairSTO_model.toString().trim() in ['', '[]']) ? clairSTO_modelMap.get(meta.basecall_model.toString().trim()) : meta.clairSTO_model @@ -29,7 +30,6 @@ workflow TUMOR_ONLY_HAPPHASE { } .set{ tumor_bams } - // // MODULE: CLAIRSTO // From 29ec483f49a667862b4780de0a6dcd1b38551326 Mon Sep 17 00:00:00 2001 From: ljwharbers Date: Thu, 27 Nov 2025 16:21:29 +0100 Subject: [PATCH 42/42] add def back in --- modules/local/clairs/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/clairs/main.nf b/modules/local/clairs/main.nf index d4368bf6..74d812f3 100644 --- a/modules/local/clairs/main.nf +++ b/modules/local/clairs/main.nf @@ -21,7 +21,7 @@ process CLAIRS { script: def args = task.ext.args ?: '' - prefix = task.ext.prefix ?: "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ /opt/bin/run_clairs \