diff --git a/main.nf b/main.nf index c47980c73..49e1bf0bd 100755 --- a/main.nf +++ b/main.nf @@ -10,6 +10,7 @@ */ nextflow.enable.dsl = 2 +nextflow.preview.topic = true /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diff --git a/modules/local/bedtools_genomecov/main.nf b/modules/local/bedtools_genomecov/main.nf index 0a0fb3c8b..a2cdb183b 100644 --- a/modules/local/bedtools_genomecov/main.nf +++ b/modules/local/bedtools_genomecov/main.nf @@ -13,7 +13,7 @@ process BEDTOOLS_GENOMECOV { output: tuple val(meta), path("*.forward.bedGraph"), emit: bedgraph_forward tuple val(meta), path("*.reverse.bedGraph"), emit: bedgraph_reverse - path "versions.yml" , emit: versions + path "versions.yml" , topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/local/cat_additional_fasta/main.nf b/modules/local/cat_additional_fasta/main.nf index 72af4bc54..05761bab2 100644 --- a/modules/local/cat_additional_fasta/main.nf +++ b/modules/local/cat_additional_fasta/main.nf @@ -15,7 +15,7 @@ process CAT_ADDITIONAL_FASTA { output: path "${name}.fasta", emit: fasta path "${name}.gtf" , emit: gtf - path "versions.yml" , emit: versions + path "versions.yml" , topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/local/deseq2_qc/main.nf b/modules/local/deseq2_qc/main.nf index 7b3fac57b..af19de7a4 100644 --- a/modules/local/deseq2_qc/main.nf +++ b/modules/local/deseq2_qc/main.nf @@ -22,7 +22,7 @@ process DESEQ2_QC { path "*sample.dists_mqc.tsv", optional:true, emit: dists_multiqc path "*.log" , optional:true, emit: log path "size_factors" , optional:true, emit: size_factors - path "versions.yml" , emit: versions + path "versions.yml" , topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/local/dupradar/main.nf b/modules/local/dupradar/main.nf index 9f9152d1e..03a90d574 100644 --- a/modules/local/dupradar/main.nf +++ b/modules/local/dupradar/main.nf @@ -15,7 +15,7 @@ process DUPRADAR { tuple val(meta), path("*.pdf") , emit: pdf tuple val(meta), path("*.txt") , emit: txt tuple val(meta), path("*_mqc.txt"), emit: multiqc - path "versions.yml" , emit: versions + path "versions.yml" , topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/local/gtf2bed/main.nf b/modules/local/gtf2bed/main.nf index 8a4bae8ff..1aedccbed 100644 --- a/modules/local/gtf2bed/main.nf +++ b/modules/local/gtf2bed/main.nf @@ -12,7 +12,7 @@ process GTF2BED { output: path '*.bed' , emit: bed - path "versions.yml", emit: versions + path "versions.yml", topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/local/gtf_gene_filter/main.nf b/modules/local/gtf_gene_filter/main.nf index cd8e16adb..03621eaf3 100644 --- a/modules/local/gtf_gene_filter/main.nf +++ b/modules/local/gtf_gene_filter/main.nf @@ -12,7 +12,7 @@ process GTF_GENE_FILTER { output: path "*.gtf" , emit: gtf - path "versions.yml", emit: versions + path "versions.yml", topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/local/multiqc_custom_biotype/main.nf b/modules/local/multiqc_custom_biotype/main.nf index 9c0fe94eb..84590eac7 100644 --- a/modules/local/multiqc_custom_biotype/main.nf +++ b/modules/local/multiqc_custom_biotype/main.nf @@ -12,7 +12,7 @@ process MULTIQC_CUSTOM_BIOTYPE { output: tuple val(meta), path("*.tsv"), emit: tsv - path "versions.yml" , emit: versions + path "versions.yml" , topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/local/preprocess_transcripts_fasta_gencode/main.nf b/modules/local/preprocess_transcripts_fasta_gencode/main.nf index 41f1d42f6..101b8adb0 100644 --- a/modules/local/preprocess_transcripts_fasta_gencode/main.nf +++ b/modules/local/preprocess_transcripts_fasta_gencode/main.nf @@ -11,7 +11,7 @@ process PREPROCESS_TRANSCRIPTS_FASTA_GENCODE { output: path "*.fa" , emit: fasta - path "versions.yml", emit: versions + path "versions.yml", topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/local/rsem_merge_counts/main.nf b/modules/local/rsem_merge_counts/main.nf index 3f226f54d..8071db83f 100644 --- a/modules/local/rsem_merge_counts/main.nf +++ b/modules/local/rsem_merge_counts/main.nf @@ -15,7 +15,7 @@ process RSEM_MERGE_COUNTS { path "rsem.merged.gene_tpm.tsv" , emit: tpm_gene path "rsem.merged.transcript_counts.tsv", emit: counts_transcript path "rsem.merged.transcript_tpm.tsv" , emit: tpm_transcript - path "versions.yml" , emit: versions + path "versions.yml" , topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/local/salmon_summarizedexperiment/main.nf b/modules/local/salmon_summarizedexperiment/main.nf index 2278ea14e..fb0d940f1 100644 --- a/modules/local/salmon_summarizedexperiment/main.nf +++ b/modules/local/salmon_summarizedexperiment/main.nf @@ -14,7 +14,7 @@ process SALMON_SUMMARIZEDEXPERIMENT { output: path "*.rds" , emit: rds - path "versions.yml", emit: versions + path "versions.yml", topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/local/salmon_tx2gene/main.nf b/modules/local/salmon_tx2gene/main.nf index b6e9df662..5292c511c 100644 --- a/modules/local/salmon_tx2gene/main.nf +++ b/modules/local/salmon_tx2gene/main.nf @@ -13,7 +13,7 @@ process SALMON_TX2GENE { output: path "*.tsv" , emit: tsv - path "versions.yml", emit: versions + path "versions.yml", topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/local/salmon_tximport/main.nf b/modules/local/salmon_tximport/main.nf index 181c897cd..4938c889a 100644 --- a/modules/local/salmon_tximport/main.nf +++ b/modules/local/salmon_tximport/main.nf @@ -17,7 +17,7 @@ process SALMON_TXIMPORT { path "*gene_counts_scaled.tsv" , emit: counts_gene_scaled path "*transcript_tpm.tsv" , emit: tpm_transcript path "*transcript_counts.tsv" , emit: counts_transcript - path "versions.yml" , emit: versions + path "versions.yml" , topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/local/star_align_igenomes/main.nf b/modules/local/star_align_igenomes/main.nf index 3e5a169d8..dd64f1839 100644 --- a/modules/local/star_align_igenomes/main.nf +++ b/modules/local/star_align_igenomes/main.nf @@ -20,7 +20,7 @@ process STAR_ALIGN_IGENOMES { tuple val(meta), path('*Log.final.out') , emit: log_final tuple val(meta), path('*Log.out') , emit: log_out tuple val(meta), path('*Log.progress.out'), emit: log_progress - path "versions.yml" , emit: versions + path "versions.yml" , topic: versions tuple val(meta), path('*sortedByCoord.out.bam') , optional:true, emit: bam_sorted tuple val(meta), path('*toTranscriptome.out.bam'), optional:true, emit: bam_transcript diff --git a/modules/local/star_genomegenerate_igenomes/main.nf b/modules/local/star_genomegenerate_igenomes/main.nf index 7766faaaf..aebd910fc 100644 --- a/modules/local/star_genomegenerate_igenomes/main.nf +++ b/modules/local/star_genomegenerate_igenomes/main.nf @@ -13,7 +13,7 @@ process STAR_GENOMEGENERATE_IGENOMES { output: path "star" , emit: index - path "versions.yml", emit: versions + path "versions.yml", topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/local/umitools_prepareforrsem/main.nf b/modules/local/umitools_prepareforrsem/main.nf index 9ee41737d..7162236c0 100644 --- a/modules/local/umitools_prepareforrsem/main.nf +++ b/modules/local/umitools_prepareforrsem/main.nf @@ -13,7 +13,7 @@ process UMITOOLS_PREPAREFORRSEM { output: tuple val(meta), path('*.bam'), emit: bam tuple val(meta), path('*.log'), emit: log - path "versions.yml" , emit: versions + path "versions.yml" , topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/bbmap/bbsplit/main.nf b/modules/nf-core/bbmap/bbsplit/main.nf index f82bb9e47..e1f1b1809 100644 --- a/modules/nf-core/bbmap/bbsplit/main.nf +++ b/modules/nf-core/bbmap/bbsplit/main.nf @@ -20,7 +20,7 @@ process BBMAP_BBSPLIT { tuple val(meta), path('*primary*fastq.gz'), optional:true, emit: primary_fastq tuple val(meta), path('*fastq.gz') , optional:true, emit: all_fastq tuple val(meta), path('*txt') , optional:true, emit: stats - path "versions.yml" , emit: versions + path "versions.yml" , topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf index 5021e6fcb..88b3fc51e 100644 --- a/modules/nf-core/cat/fastq/main.nf +++ b/modules/nf-core/cat/fastq/main.nf @@ -12,7 +12,7 @@ process CAT_FASTQ { output: tuple val(meta), path("*.merged.fastq.gz"), emit: reads - path "versions.yml" , emit: versions + path "versions.yml" , topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/custom/getchromsizes/main.nf b/modules/nf-core/custom/getchromsizes/main.nf index 060a2e885..39b48542d 100644 --- a/modules/nf-core/custom/getchromsizes/main.nf +++ b/modules/nf-core/custom/getchromsizes/main.nf @@ -14,7 +14,7 @@ process CUSTOM_GETCHROMSIZES { tuple val(meta), path ("*.sizes"), emit: sizes tuple val(meta), path ("*.fai") , emit: fai tuple val(meta), path ("*.gzi") , emit: gzi, optional: true - path "versions.yml" , emit: versions + path "versions.yml" , topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/fastp/main.nf b/modules/nf-core/fastp/main.nf index 831b7f128..b58a0bab3 100644 --- a/modules/nf-core/fastp/main.nf +++ b/modules/nf-core/fastp/main.nf @@ -18,7 +18,7 @@ process FASTP { tuple val(meta), path('*.json') , emit: json tuple val(meta), path('*.html') , emit: html tuple val(meta), path('*.log') , emit: log - path "versions.yml" , emit: versions + path "versions.yml" , topic: versions tuple val(meta), path('*.fail.fastq.gz') , optional:true, emit: reads_fail tuple val(meta), path('*.merged.fastq.gz'), optional:true, emit: reads_merged diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index 67209f793..a4d015378 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -13,7 +13,7 @@ process FASTQC { output: tuple val(meta), path("*.html"), emit: html tuple val(meta), path("*.zip") , emit: zip - path "versions.yml" , emit: versions + path "versions.yml" , topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/fq/subsample/main.nf b/modules/nf-core/fq/subsample/main.nf index 8b4ff5be0..4c887d18d 100644 --- a/modules/nf-core/fq/subsample/main.nf +++ b/modules/nf-core/fq/subsample/main.nf @@ -12,7 +12,7 @@ process FQ_SUBSAMPLE { output: tuple val(meta), path("*.fastq.gz"), emit: fastq - path "versions.yml" , emit: versions + path "versions.yml" , topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/gffread/main.nf b/modules/nf-core/gffread/main.nf index f4472b0e8..baba16513 100644 --- a/modules/nf-core/gffread/main.nf +++ b/modules/nf-core/gffread/main.nf @@ -12,7 +12,7 @@ process GFFREAD { output: path "*.gtf" , emit: gtf - path "versions.yml" , emit: versions + path "versions.yml" , topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/gunzip/main.nf b/modules/nf-core/gunzip/main.nf index 73bf08cde..7003bb478 100644 --- a/modules/nf-core/gunzip/main.nf +++ b/modules/nf-core/gunzip/main.nf @@ -12,7 +12,7 @@ process GUNZIP { output: tuple val(meta), path("$gunzip"), emit: gunzip - path "versions.yml" , emit: versions + path "versions.yml" , topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/hisat2/align/main.nf b/modules/nf-core/hisat2/align/main.nf index db8e8bb6d..e95d3d2bf 100644 --- a/modules/nf-core/hisat2/align/main.nf +++ b/modules/nf-core/hisat2/align/main.nf @@ -17,7 +17,7 @@ process HISAT2_ALIGN { tuple val(meta), path("*.bam") , emit: bam tuple val(meta), path("*.log") , emit: summary tuple val(meta), path("*fastq.gz"), optional:true, emit: fastq - path "versions.yml" , emit: versions + path "versions.yml" , topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/hisat2/build/main.nf b/modules/nf-core/hisat2/build/main.nf index 90f8efcc6..f295639e5 100644 --- a/modules/nf-core/hisat2/build/main.nf +++ b/modules/nf-core/hisat2/build/main.nf @@ -16,7 +16,7 @@ process HISAT2_BUILD { output: tuple val(meta), path("hisat2") , emit: index - path "versions.yml" , emit: versions + path "versions.yml" , topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/hisat2/extractsplicesites/main.nf b/modules/nf-core/hisat2/extractsplicesites/main.nf index a6e59e202..0d625944a 100644 --- a/modules/nf-core/hisat2/extractsplicesites/main.nf +++ b/modules/nf-core/hisat2/extractsplicesites/main.nf @@ -13,7 +13,7 @@ process HISAT2_EXTRACTSPLICESITES { output: tuple val(meta), path("*.splice_sites.txt"), emit: txt - path "versions.yml" , emit: versions + path "versions.yml" , topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/picard/markduplicates/main.nf b/modules/nf-core/picard/markduplicates/main.nf index ebfa0864d..79225e34a 100644 --- a/modules/nf-core/picard/markduplicates/main.nf +++ b/modules/nf-core/picard/markduplicates/main.nf @@ -16,7 +16,7 @@ process PICARD_MARKDUPLICATES { tuple val(meta), path("*.bam") , emit: bam tuple val(meta), path("*.bai") , optional:true, emit: bai tuple val(meta), path("*.metrics.txt"), emit: metrics - path "versions.yml" , emit: versions + path "versions.yml" , topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/preseq/lcextrap/main.nf b/modules/nf-core/preseq/lcextrap/main.nf index 12546f0a2..ec7cf08b4 100644 --- a/modules/nf-core/preseq/lcextrap/main.nf +++ b/modules/nf-core/preseq/lcextrap/main.nf @@ -14,7 +14,7 @@ process PRESEQ_LCEXTRAP { output: tuple val(meta), path("*.lc_extrap.txt"), emit: lc_extrap tuple val(meta), path("*.log") , emit: log - path "versions.yml" , emit: versions + path "versions.yml" , topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/qualimap/rnaseq/main.nf b/modules/nf-core/qualimap/rnaseq/main.nf index 044c983fc..a5082a8e2 100644 --- a/modules/nf-core/qualimap/rnaseq/main.nf +++ b/modules/nf-core/qualimap/rnaseq/main.nf @@ -13,7 +13,7 @@ process QUALIMAP_RNASEQ { output: tuple val(meta), path("${prefix}"), emit: results - path "versions.yml" , emit: versions + path "versions.yml" , topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/rsem/calculateexpression/main.nf b/modules/nf-core/rsem/calculateexpression/main.nf index 54041aedb..601b61b98 100644 --- a/modules/nf-core/rsem/calculateexpression/main.nf +++ b/modules/nf-core/rsem/calculateexpression/main.nf @@ -16,7 +16,7 @@ process RSEM_CALCULATEEXPRESSION { tuple val(meta), path("*.isoforms.results"), emit: counts_transcript tuple val(meta), path("*.stat") , emit: stat tuple val(meta), path("*.log") , emit: logs - path "versions.yml" , emit: versions + path "versions.yml" , topic: versions tuple val(meta), path("*.STAR.genome.bam") , optional:true, emit: bam_star tuple val(meta), path("${prefix}.genome.bam") , optional:true, emit: bam_genome diff --git a/modules/nf-core/rsem/preparereference/main.nf b/modules/nf-core/rsem/preparereference/main.nf index 62b93d08a..ef0295f01 100644 --- a/modules/nf-core/rsem/preparereference/main.nf +++ b/modules/nf-core/rsem/preparereference/main.nf @@ -14,7 +14,7 @@ process RSEM_PREPAREREFERENCE { output: path "rsem" , emit: index path "*transcripts.fa", emit: transcript_fasta - path "versions.yml" , emit: versions + path "versions.yml" , topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/rseqc/bamstat/main.nf b/modules/nf-core/rseqc/bamstat/main.nf index 04c1eefd0..75ccb8199 100644 --- a/modules/nf-core/rseqc/bamstat/main.nf +++ b/modules/nf-core/rseqc/bamstat/main.nf @@ -12,7 +12,7 @@ process RSEQC_BAMSTAT { output: tuple val(meta), path("*.bam_stat.txt"), emit: txt - path "versions.yml" , emit: versions + path "versions.yml" , topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/rseqc/inferexperiment/main.nf b/modules/nf-core/rseqc/inferexperiment/main.nf index 5f9f4b111..d6e7c4f61 100644 --- a/modules/nf-core/rseqc/inferexperiment/main.nf +++ b/modules/nf-core/rseqc/inferexperiment/main.nf @@ -13,7 +13,7 @@ process RSEQC_INFEREXPERIMENT { output: tuple val(meta), path("*.infer_experiment.txt"), emit: txt - path "versions.yml" , emit: versions + path "versions.yml" , topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/rseqc/innerdistance/main.nf b/modules/nf-core/rseqc/innerdistance/main.nf index a63a2bf03..bce826128 100644 --- a/modules/nf-core/rseqc/innerdistance/main.nf +++ b/modules/nf-core/rseqc/innerdistance/main.nf @@ -17,7 +17,7 @@ process RSEQC_INNERDISTANCE { tuple val(meta), path("*mean.txt") , optional:true, emit: mean tuple val(meta), path("*.pdf") , optional:true, emit: pdf tuple val(meta), path("*.r") , optional:true, emit: rscript - path "versions.yml" , emit: versions + path "versions.yml" , topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/rseqc/junctionannotation/main.nf b/modules/nf-core/rseqc/junctionannotation/main.nf index 4029ac765..39bf7e9b2 100644 --- a/modules/nf-core/rseqc/junctionannotation/main.nf +++ b/modules/nf-core/rseqc/junctionannotation/main.nf @@ -19,7 +19,7 @@ process RSEQC_JUNCTIONANNOTATION { tuple val(meta), path("*.Interact.bed"), optional:true, emit: interact_bed tuple val(meta), path("*junction.pdf") , optional:true, emit: pdf tuple val(meta), path("*events.pdf") , optional:true, emit: events_pdf - path "versions.yml" , emit: versions + path "versions.yml" , topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/rseqc/junctionsaturation/main.nf b/modules/nf-core/rseqc/junctionsaturation/main.nf index 93cc61b23..aed9194d3 100644 --- a/modules/nf-core/rseqc/junctionsaturation/main.nf +++ b/modules/nf-core/rseqc/junctionsaturation/main.nf @@ -14,7 +14,7 @@ process RSEQC_JUNCTIONSATURATION { output: tuple val(meta), path("*.pdf"), emit: pdf tuple val(meta), path("*.r") , emit: rscript - path "versions.yml" , emit: versions + path "versions.yml" , topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/rseqc/readdistribution/main.nf b/modules/nf-core/rseqc/readdistribution/main.nf index f3e588d69..c38a1d9c1 100644 --- a/modules/nf-core/rseqc/readdistribution/main.nf +++ b/modules/nf-core/rseqc/readdistribution/main.nf @@ -13,7 +13,7 @@ process RSEQC_READDISTRIBUTION { output: tuple val(meta), path("*.read_distribution.txt"), emit: txt - path "versions.yml" , emit: versions + path "versions.yml" , topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/rseqc/readduplication/main.nf b/modules/nf-core/rseqc/readduplication/main.nf index 023118536..08febbc5c 100644 --- a/modules/nf-core/rseqc/readduplication/main.nf +++ b/modules/nf-core/rseqc/readduplication/main.nf @@ -15,7 +15,7 @@ process RSEQC_READDUPLICATION { tuple val(meta), path("*pos.DupRate.xls"), emit: pos_xls tuple val(meta), path("*.pdf") , emit: pdf tuple val(meta), path("*.r") , emit: rscript - path "versions.yml" , emit: versions + path "versions.yml" , topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/rseqc/tin/main.nf b/modules/nf-core/rseqc/tin/main.nf index 872938b62..befab7dc3 100644 --- a/modules/nf-core/rseqc/tin/main.nf +++ b/modules/nf-core/rseqc/tin/main.nf @@ -14,7 +14,7 @@ process RSEQC_TIN { output: tuple val(meta), path("*.txt"), emit: txt tuple val(meta), path("*.xls"), emit: xls - path "versions.yml" , emit: versions + path "versions.yml" , topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/salmon/index/main.nf b/modules/nf-core/salmon/index/main.nf index 118ee6704..0d2fed5c4 100644 --- a/modules/nf-core/salmon/index/main.nf +++ b/modules/nf-core/salmon/index/main.nf @@ -13,7 +13,7 @@ process SALMON_INDEX { output: path "salmon" , emit: index - path "versions.yml", emit: versions + path "versions.yml", topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/salmon/quant/main.nf b/modules/nf-core/salmon/quant/main.nf index f11b6c2e2..6caaccaf1 100644 --- a/modules/nf-core/salmon/quant/main.nf +++ b/modules/nf-core/salmon/quant/main.nf @@ -18,7 +18,7 @@ process SALMON_QUANT { output: tuple val(meta), path("${prefix}") , emit: results tuple val(meta), path("*info.json"), emit: json_info, optional: true - path "versions.yml" , emit: versions + path "versions.yml" , topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/samtools/flagstat/main.nf b/modules/nf-core/samtools/flagstat/main.nf index b75707eca..b7cf31c9f 100644 --- a/modules/nf-core/samtools/flagstat/main.nf +++ b/modules/nf-core/samtools/flagstat/main.nf @@ -12,7 +12,7 @@ process SAMTOOLS_FLAGSTAT { output: tuple val(meta), path("*.flagstat"), emit: flagstat - path "versions.yml" , emit: versions + path "versions.yml" , topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/samtools/idxstats/main.nf b/modules/nf-core/samtools/idxstats/main.nf index 83c7c34b9..3c1dff77e 100644 --- a/modules/nf-core/samtools/idxstats/main.nf +++ b/modules/nf-core/samtools/idxstats/main.nf @@ -12,7 +12,7 @@ process SAMTOOLS_IDXSTATS { output: tuple val(meta), path("*.idxstats"), emit: idxstats - path "versions.yml" , emit: versions + path "versions.yml" , topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf index 0b20aa4bb..153d40a27 100644 --- a/modules/nf-core/samtools/index/main.nf +++ b/modules/nf-core/samtools/index/main.nf @@ -14,7 +14,7 @@ process SAMTOOLS_INDEX { 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 + path "versions.yml" , topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf index 2b7753fd8..3784ca87f 100644 --- a/modules/nf-core/samtools/sort/main.nf +++ b/modules/nf-core/samtools/sort/main.nf @@ -13,7 +13,7 @@ process SAMTOOLS_SORT { output: tuple val(meta), path("*.bam"), emit: bam tuple val(meta), path("*.csi"), emit: csi, optional: true - path "versions.yml" , emit: versions + path "versions.yml" , topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/samtools/stats/main.nf b/modules/nf-core/samtools/stats/main.nf index 4a2607ded..fa3f2d18f 100644 --- a/modules/nf-core/samtools/stats/main.nf +++ b/modules/nf-core/samtools/stats/main.nf @@ -13,7 +13,7 @@ process SAMTOOLS_STATS { output: tuple val(meta), path("*.stats"), emit: stats - path "versions.yml" , emit: versions + path "versions.yml" , topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/sortmerna/main.nf b/modules/nf-core/sortmerna/main.nf index 7afae5a68..30faa6e71 100644 --- a/modules/nf-core/sortmerna/main.nf +++ b/modules/nf-core/sortmerna/main.nf @@ -14,7 +14,7 @@ process SORTMERNA { output: tuple val(meta), path("*non_rRNA.fastq.gz"), emit: reads tuple val(meta), path("*.log") , emit: log - path "versions.yml" , emit: versions + path "versions.yml" , topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/star/align/main.nf b/modules/nf-core/star/align/main.nf index d0e203848..ad2d8addf 100644 --- a/modules/nf-core/star/align/main.nf +++ b/modules/nf-core/star/align/main.nf @@ -19,7 +19,7 @@ process STAR_ALIGN { tuple val(meta), path('*Log.final.out') , emit: log_final tuple val(meta), path('*Log.out') , emit: log_out tuple val(meta), path('*Log.progress.out'), emit: log_progress - path "versions.yml" , emit: versions + path "versions.yml" , topic: versions tuple val(meta), path('*d.out.bam') , optional:true, emit: bam tuple val(meta), path('*sortedByCoord.out.bam') , optional:true, emit: bam_sorted diff --git a/modules/nf-core/star/genomegenerate/main.nf b/modules/nf-core/star/genomegenerate/main.nf index 434240427..0e10abdba 100644 --- a/modules/nf-core/star/genomegenerate/main.nf +++ b/modules/nf-core/star/genomegenerate/main.nf @@ -13,7 +13,7 @@ process STAR_GENOMEGENERATE { output: tuple val(meta), path("star") , emit: index - path "versions.yml" , emit: versions + path "versions.yml" , topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/stringtie/stringtie/main.nf b/modules/nf-core/stringtie/stringtie/main.nf index d0f8b563f..9c9d91d54 100644 --- a/modules/nf-core/stringtie/stringtie/main.nf +++ b/modules/nf-core/stringtie/stringtie/main.nf @@ -16,7 +16,7 @@ process STRINGTIE_STRINGTIE { tuple val(meta), path("*.abundance.txt") , emit: abundance tuple val(meta), path("*.coverage.gtf") , optional: true, emit: coverage_gtf tuple val(meta), path("*.ballgown") , optional: true, emit: ballgown - path "versions.yml" , emit: versions + path "versions.yml" , topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/subread/featurecounts/main.nf b/modules/nf-core/subread/featurecounts/main.nf index a524b92f1..e0fb5a3af 100644 --- a/modules/nf-core/subread/featurecounts/main.nf +++ b/modules/nf-core/subread/featurecounts/main.nf @@ -13,7 +13,7 @@ process SUBREAD_FEATURECOUNTS { output: tuple val(meta), path("*featureCounts.txt") , emit: counts tuple val(meta), path("*featureCounts.txt.summary"), emit: summary - path "versions.yml" , emit: versions + path "versions.yml" , topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/trimgalore/main.nf b/modules/nf-core/trimgalore/main.nf index dcb77ae7b..169d0e627 100644 --- a/modules/nf-core/trimgalore/main.nf +++ b/modules/nf-core/trimgalore/main.nf @@ -16,7 +16,7 @@ process TRIMGALORE { tuple val(meta), path("*unpaired*.fq.gz") , emit: unpaired, optional: true tuple val(meta), path("*.html") , emit: html , optional: true tuple val(meta), path("*.zip") , emit: zip , optional: true - path "versions.yml" , emit: versions + path "versions.yml" , topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/ucsc/bedclip/main.nf b/modules/nf-core/ucsc/bedclip/main.nf index 4bad9a399..95c4be49f 100755 --- a/modules/nf-core/ucsc/bedclip/main.nf +++ b/modules/nf-core/ucsc/bedclip/main.nf @@ -14,7 +14,7 @@ process UCSC_BEDCLIP { output: tuple val(meta), path("*.bedGraph"), emit: bedgraph - path "versions.yml" , emit: versions + path "versions.yml" , topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/ucsc/bedgraphtobigwig/main.nf b/modules/nf-core/ucsc/bedgraphtobigwig/main.nf index 06bb47099..a0c989887 100644 --- a/modules/nf-core/ucsc/bedgraphtobigwig/main.nf +++ b/modules/nf-core/ucsc/bedgraphtobigwig/main.nf @@ -14,7 +14,7 @@ process UCSC_BEDGRAPHTOBIGWIG { output: tuple val(meta), path("*.bigWig"), emit: bigwig - path "versions.yml" , emit: versions + path "versions.yml" , topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/umitools/dedup/main.nf b/modules/nf-core/umitools/dedup/main.nf index 56ea04691..65fe2ab22 100644 --- a/modules/nf-core/umitools/dedup/main.nf +++ b/modules/nf-core/umitools/dedup/main.nf @@ -17,7 +17,7 @@ process UMITOOLS_DEDUP { tuple val(meta), path("*edit_distance.tsv"), optional:true, emit: tsv_edit_distance tuple val(meta), path("*per_umi.tsv") , optional:true, emit: tsv_per_umi tuple val(meta), path("*per_position.tsv") , optional:true, emit: tsv_umi_per_position - path "versions.yml" , emit: versions + path "versions.yml" , topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/umitools/extract/main.nf b/modules/nf-core/umitools/extract/main.nf index 2f94fa93e..6816f1c98 100644 --- a/modules/nf-core/umitools/extract/main.nf +++ b/modules/nf-core/umitools/extract/main.nf @@ -14,7 +14,7 @@ process UMITOOLS_EXTRACT { output: tuple val(meta), path("*.fastq.gz"), emit: reads tuple val(meta), path("*.log") , emit: log - path "versions.yml" , emit: versions + path "versions.yml" , topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf index 61461c391..4f96f031a 100644 --- a/modules/nf-core/untar/main.nf +++ b/modules/nf-core/untar/main.nf @@ -12,7 +12,7 @@ process UNTAR { output: tuple val(meta), path("$prefix"), emit: untar - path "versions.yml" , emit: versions + path "versions.yml" , topic: versions when: task.ext.when == null || task.ext.when diff --git a/subworkflows/local/align_star/main.nf b/subworkflows/local/align_star/main.nf index 1dba0c085..d52c907b7 100644 --- a/subworkflows/local/align_star/main.nf +++ b/subworkflows/local/align_star/main.nf @@ -18,9 +18,6 @@ workflow ALIGN_STAR { fasta // channel: /path/to/fasta main: - - ch_versions = Channel.empty() - // // Map reads with STAR // @@ -42,7 +39,6 @@ workflow ALIGN_STAR { ch_bam_transcript = STAR_ALIGN_IGENOMES.out.bam_transcript ch_fastq = STAR_ALIGN_IGENOMES.out.fastq ch_tab = STAR_ALIGN_IGENOMES.out.tab - ch_versions = ch_versions.mix(STAR_ALIGN_IGENOMES.out.versions.first()) } else { STAR_ALIGN ( reads, index, gtf, star_ignore_sjdbgtf, seq_platform, seq_center ) ch_orig_bam = STAR_ALIGN.out.bam @@ -53,14 +49,12 @@ workflow ALIGN_STAR { ch_bam_transcript = STAR_ALIGN.out.bam_transcript ch_fastq = STAR_ALIGN.out.fastq ch_tab = STAR_ALIGN.out.tab - ch_versions = ch_versions.mix(STAR_ALIGN.out.versions.first()) } // // Sort, index BAM file and run samtools stats, flagstat and idxstats // BAM_SORT_STATS_SAMTOOLS ( ch_orig_bam, fasta ) - ch_versions = ch_versions.mix(BAM_SORT_STATS_SAMTOOLS.out.versions) emit: orig_bam = ch_orig_bam // channel: [ val(meta), bam ] @@ -78,6 +72,4 @@ workflow ALIGN_STAR { stats = BAM_SORT_STATS_SAMTOOLS.out.stats // channel: [ val(meta), [ stats ] ] flagstat = BAM_SORT_STATS_SAMTOOLS.out.flagstat // channel: [ val(meta), [ flagstat ] ] idxstats = BAM_SORT_STATS_SAMTOOLS.out.idxstats // channel: [ val(meta), [ idxstats ] ] - - versions = ch_versions // channel: [ versions.yml ] } diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf index eceb2c1ce..9135c1d23 100644 --- a/subworkflows/local/prepare_genome/main.nf +++ b/subworkflows/local/prepare_genome/main.nf @@ -52,15 +52,11 @@ workflow PREPARE_GENOME { prepare_tool_indices // list: tools to prepare indices for main: - - ch_versions = Channel.empty() - // // Uncompress genome fasta file if required // if (fasta.endsWith('.gz')) { ch_fasta = GUNZIP_FASTA ( [ [:], fasta ] ).gunzip.map { it[1] } - ch_versions = ch_versions.mix(GUNZIP_FASTA.out.versions) } else { ch_fasta = Channel.value(file(fasta)) } @@ -71,19 +67,16 @@ workflow PREPARE_GENOME { if (gtf) { if (gtf.endsWith('.gz')) { ch_gtf = GUNZIP_GTF ( [ [:], gtf ] ).gunzip.map { it[1] } - ch_versions = ch_versions.mix(GUNZIP_GTF.out.versions) } else { ch_gtf = Channel.value(file(gtf)) } } else if (gff) { if (gff.endsWith('.gz')) { ch_gff = GUNZIP_GFF ( [ [:], gff ] ).gunzip.map { it[1] } - ch_versions = ch_versions.mix(GUNZIP_GFF.out.versions) } else { ch_gff = Channel.value(file(gff)) } ch_gtf = GFFREAD ( ch_gff ).gtf - ch_versions = ch_versions.mix(GFFREAD.out.versions) } // @@ -92,14 +85,12 @@ workflow PREPARE_GENOME { if (additional_fasta) { if (additional_fasta.endsWith('.gz')) { ch_add_fasta = GUNZIP_ADDITIONAL_FASTA ( [ [:], additional_fasta ] ).gunzip.map { it[1] } - ch_versions = ch_versions.mix(GUNZIP_ADDITIONAL_FASTA.out.versions) } else { ch_add_fasta = Channel.value(file(additional_fasta)) } CAT_ADDITIONAL_FASTA ( ch_fasta, ch_gtf, ch_add_fasta, biotype ) ch_fasta = CAT_ADDITIONAL_FASTA.out.fasta ch_gtf = CAT_ADDITIONAL_FASTA.out.gtf - ch_versions = ch_versions.mix(CAT_ADDITIONAL_FASTA.out.versions) } // @@ -108,13 +99,11 @@ workflow PREPARE_GENOME { if (gene_bed) { if (gene_bed.endsWith('.gz')) { ch_gene_bed = GUNZIP_GENE_BED ( [ [:], gene_bed ] ).gunzip.map { it[1] } - ch_versions = ch_versions.mix(GUNZIP_GENE_BED.out.versions) } else { ch_gene_bed = Channel.value(file(gene_bed)) } } else { ch_gene_bed = GTF2BED ( ch_gtf ).bed - ch_versions = ch_versions.mix(GTF2BED.out.versions) } // @@ -123,20 +112,16 @@ workflow PREPARE_GENOME { if (transcript_fasta) { if (transcript_fasta.endsWith('.gz')) { ch_transcript_fasta = GUNZIP_TRANSCRIPT_FASTA ( [ [:], transcript_fasta ] ).gunzip.map { it[1] } - ch_versions = ch_versions.mix(GUNZIP_TRANSCRIPT_FASTA.out.versions) } else { ch_transcript_fasta = Channel.value(file(transcript_fasta)) } if (gencode) { PREPROCESS_TRANSCRIPTS_FASTA_GENCODE ( ch_transcript_fasta ) ch_transcript_fasta = PREPROCESS_TRANSCRIPTS_FASTA_GENCODE.out.fasta - ch_versions = ch_versions.mix(PREPROCESS_TRANSCRIPTS_FASTA_GENCODE.out.versions) } } else { ch_filter_gtf = GTF_GENE_FILTER ( ch_fasta, ch_gtf ).gtf ch_transcript_fasta = MAKE_TRANSCRIPTS_FASTA ( ch_fasta, ch_filter_gtf ).transcript_fasta - ch_versions = ch_versions.mix(GTF_GENE_FILTER.out.versions) - ch_versions = ch_versions.mix(MAKE_TRANSCRIPTS_FASTA.out.versions) } // @@ -145,7 +130,6 @@ workflow PREPARE_GENOME { CUSTOM_GETCHROMSIZES ( ch_fasta.map { [ [:], it ] } ) ch_fai = CUSTOM_GETCHROMSIZES.out.fai.map { it[1] } ch_chrom_sizes = CUSTOM_GETCHROMSIZES.out.sizes.map { it[1] } - ch_versions = ch_versions.mix(CUSTOM_GETCHROMSIZES.out.versions) // // Uncompress BBSplit index or generate from scratch if required @@ -155,7 +139,6 @@ workflow PREPARE_GENOME { if (bbsplit_index) { if (bbsplit_index.endsWith('.tar.gz')) { ch_bbsplit_index = UNTAR_BBSPLIT_INDEX ( [ [:], bbsplit_index ] ).untar.map { it[1] } - ch_versions = ch_versions.mix(UNTAR_BBSPLIT_INDEX.out.versions) } else { ch_bbsplit_index = Channel.value(file(bbsplit_index)) } @@ -170,7 +153,6 @@ workflow PREPARE_GENOME { .set { ch_bbsplit_fasta_list } ch_bbsplit_index = BBMAP_BBSPLIT ( [ [:], [] ], [], ch_fasta, ch_bbsplit_fasta_list, true ).index - ch_versions = ch_versions.mix(BBMAP_BBSPLIT.out.versions) } } @@ -182,17 +164,14 @@ workflow PREPARE_GENOME { if (star_index) { if (star_index.endsWith('.tar.gz')) { ch_star_index = UNTAR_STAR_INDEX ( [ [:], star_index ] ).untar.map { it[1] } - ch_versions = ch_versions.mix(UNTAR_STAR_INDEX.out.versions) } else { ch_star_index = Channel.value(file(star_index)) } } else { if (is_aws_igenome) { ch_star_index = STAR_GENOMEGENERATE_IGENOMES ( ch_fasta, ch_gtf ).index - ch_versions = ch_versions.mix(STAR_GENOMEGENERATE_IGENOMES.out.versions) } else { ch_star_index = STAR_GENOMEGENERATE ( ch_fasta.map { [ [:], it ] }, ch_gtf.map { [ [:], it ] } ).index.map { it[1] } - ch_versions = ch_versions.mix(STAR_GENOMEGENERATE.out.versions) } } } @@ -205,13 +184,11 @@ workflow PREPARE_GENOME { if (rsem_index) { if (rsem_index.endsWith('.tar.gz')) { ch_rsem_index = UNTAR_RSEM_INDEX ( [ [:], rsem_index ] ).untar.map { it[1] } - ch_versions = ch_versions.mix(UNTAR_RSEM_INDEX.out.versions) } else { ch_rsem_index = Channel.value(file(rsem_index)) } } else { ch_rsem_index = RSEM_PREPAREREFERENCE_GENOME ( ch_fasta, ch_gtf ).index - ch_versions = ch_versions.mix(RSEM_PREPAREREFERENCE_GENOME.out.versions) } } @@ -223,20 +200,17 @@ workflow PREPARE_GENOME { if ('hisat2' in prepare_tool_indices) { if (!splicesites) { ch_splicesites = HISAT2_EXTRACTSPLICESITES ( ch_gtf.map { [ [:], it ] } ).txt.map { it[1] } - ch_versions = ch_versions.mix(HISAT2_EXTRACTSPLICESITES.out.versions) } else { ch_splicesites = Channel.value(file(splicesites)) } if (hisat2_index) { if (hisat2_index.endsWith('.tar.gz')) { ch_hisat2_index = UNTAR_HISAT2_INDEX ( [ [:], hisat2_index ] ).untar.map { it[1] } - ch_versions = ch_versions.mix(UNTAR_HISAT2_INDEX.out.versions) } else { ch_hisat2_index = Channel.value(file(hisat2_index)) } } else { ch_hisat2_index = HISAT2_BUILD ( ch_fasta.map { [ [:], it ] }, ch_gtf.map { [ [:], it ] }, ch_splicesites.map { [ [:], it ] } ).index.map { it[1] } - ch_versions = ch_versions.mix(HISAT2_BUILD.out.versions) } } @@ -247,14 +221,12 @@ workflow PREPARE_GENOME { if (salmon_index) { if (salmon_index.endsWith('.tar.gz')) { ch_salmon_index = UNTAR_SALMON_INDEX ( [ [:], salmon_index ] ).untar.map { it[1] } - ch_versions = ch_versions.mix(UNTAR_SALMON_INDEX.out.versions) } else { ch_salmon_index = Channel.value(file(salmon_index)) } } else { if ('salmon' in prepare_tool_indices) { ch_salmon_index = SALMON_INDEX ( ch_fasta, ch_transcript_fasta ).index - ch_versions = ch_versions.mix(SALMON_INDEX.out.versions) } } @@ -271,6 +243,4 @@ workflow PREPARE_GENOME { rsem_index = ch_rsem_index // channel: path(rsem/index/) hisat2_index = ch_hisat2_index // channel: path(hisat2/index/) salmon_index = ch_salmon_index // channel: path(salmon/index/) - - versions = ch_versions.ifEmpty(null) // channel: [ versions.yml ] } diff --git a/subworkflows/local/quantify_rsem/main.nf b/subworkflows/local/quantify_rsem/main.nf index 4b7473634..8aa989b73 100644 --- a/subworkflows/local/quantify_rsem/main.nf +++ b/subworkflows/local/quantify_rsem/main.nf @@ -13,20 +13,15 @@ workflow QUANTIFY_RSEM { fasta // channel: [ val(meta), [ fasta ] ] main: - - ch_versions = Channel.empty() - // // Quantify reads with RSEM // RSEM_CALCULATEEXPRESSION ( reads, index ) - ch_versions = ch_versions.mix(RSEM_CALCULATEEXPRESSION.out.versions.first()) // // Sort, index BAM file and run samtools stats, flagstat and idxstats // BAM_SORT_STATS_SAMTOOLS ( RSEM_CALCULATEEXPRESSION.out.bam_star, fasta ) - ch_versions = ch_versions.mix(BAM_SORT_STATS_SAMTOOLS.out.versions) // // Merge counts across samples @@ -35,7 +30,6 @@ workflow QUANTIFY_RSEM { RSEM_CALCULATEEXPRESSION.out.counts_gene.collect{it[1]}, // [meta, counts]: Collect the second element (counts files) in the channel across all samples RSEM_CALCULATEEXPRESSION.out.counts_transcript.collect{it[1]} ) - ch_versions = ch_versions.mix(RSEM_MERGE_COUNTS.out.versions) emit: counts_gene = RSEM_CALCULATEEXPRESSION.out.counts_gene // channel: [ val(meta), counts ] @@ -57,6 +51,4 @@ workflow QUANTIFY_RSEM { merged_tpm_gene = RSEM_MERGE_COUNTS.out.tpm_gene // path: *.gene_tpm.tsv merged_counts_transcript = RSEM_MERGE_COUNTS.out.counts_transcript // path: *.transcript_counts.tsv merged_tpm_transcript = RSEM_MERGE_COUNTS.out.tpm_transcript // path: *.transcript_tpm.tsv - - versions = ch_versions // channel: [ versions.yml ] } diff --git a/subworkflows/local/quantify_salmon/main.nf b/subworkflows/local/quantify_salmon/main.nf index 1b936d6fe..312688afb 100644 --- a/subworkflows/local/quantify_salmon/main.nf +++ b/subworkflows/local/quantify_salmon/main.nf @@ -21,27 +21,20 @@ workflow QUANTIFY_SALMON { lib_type // val: String to override salmon library type main: - - ch_versions = Channel.empty() - // // Quantify and merge counts across samples // SALMON_QUANT ( reads, index, gtf, transcript_fasta, alignment_mode, lib_type ) - ch_versions = ch_versions.mix(SALMON_QUANT.out.versions.first()) SALMON_TX2GENE ( SALMON_QUANT.out.results.collect{it[1]}, gtf ) - ch_versions = ch_versions.mix(SALMON_TX2GENE.out.versions) SALMON_TXIMPORT ( SALMON_QUANT.out.results.collect{it[1]}, SALMON_TX2GENE.out.tsv.collect() ) - ch_versions = ch_versions.mix(SALMON_TXIMPORT.out.versions) SALMON_SE_GENE ( SALMON_TXIMPORT.out.counts_gene, SALMON_TXIMPORT.out.tpm_gene, SALMON_TX2GENE.out.tsv.collect() ) - ch_versions = ch_versions.mix(SALMON_SE_GENE.out.versions) SALMON_SE_GENE_LENGTH_SCALED ( SALMON_TXIMPORT.out.counts_gene_length_scaled, @@ -78,6 +71,4 @@ workflow QUANTIFY_SALMON { merged_counts_transcript = SALMON_TXIMPORT.out.counts_transcript // path: *.transcript_counts.tsv merged_tpm_transcript = SALMON_TXIMPORT.out.tpm_transcript // path: *.transcript_tpm.tsv merged_transcript_rds = SALMON_SE_TRANSCRIPT.out.rds // path: *.rds - - versions = ch_versions // channel: [ versions.yml ] } diff --git a/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/main.nf b/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/main.nf index 7c07084ff..dc4a5bc89 100644 --- a/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/main.nf +++ b/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/main.nf @@ -12,20 +12,15 @@ workflow BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS { val_get_dedup_stats // boolean: true/false main: - - ch_versions = Channel.empty() - // // UMI-tools dedup // UMITOOLS_DEDUP ( ch_bam_bai, val_get_dedup_stats ) - ch_versions = ch_versions.mix(UMITOOLS_DEDUP.out.versions.first()) // // Index BAM file and run samtools stats, flagstat and idxstats // SAMTOOLS_INDEX ( UMITOOLS_DEDUP.out.bam ) - ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first()) ch_bam_bai_dedup = UMITOOLS_DEDUP.out.bam .join(SAMTOOLS_INDEX.out.bai, by: [0], remainder: true) @@ -40,7 +35,6 @@ workflow BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS { } BAM_STATS_SAMTOOLS ( ch_bam_bai_dedup, [ [:], [] ] ) - ch_versions = ch_versions.mix(BAM_STATS_SAMTOOLS.out.versions) emit: bam = UMITOOLS_DEDUP.out.bam // channel: [ val(meta), path(bam) ] @@ -50,6 +44,4 @@ workflow BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS { stats = BAM_STATS_SAMTOOLS.out.stats // channel: [ val(meta), path(stats) ] flagstat = BAM_STATS_SAMTOOLS.out.flagstat // channel: [ val(meta), path(flagstat) ] idxstats = BAM_STATS_SAMTOOLS.out.idxstats // channel: [ val(meta), path(idxstats) ] - - versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/nf-core/bam_markduplicates_picard/main.nf b/subworkflows/nf-core/bam_markduplicates_picard/main.nf index 6e3df3320..cf9451f41 100644 --- a/subworkflows/nf-core/bam_markduplicates_picard/main.nf +++ b/subworkflows/nf-core/bam_markduplicates_picard/main.nf @@ -14,14 +14,9 @@ workflow BAM_MARKDUPLICATES_PICARD { ch_fai // channel: [ path(fai) ] main: - - ch_versions = Channel.empty() - PICARD_MARKDUPLICATES ( ch_bam, ch_fasta, ch_fai ) - ch_versions = ch_versions.mix(PICARD_MARKDUPLICATES.out.versions.first()) SAMTOOLS_INDEX ( PICARD_MARKDUPLICATES.out.bam ) - ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first()) ch_bam_bai = PICARD_MARKDUPLICATES.out.bam .join(SAMTOOLS_INDEX.out.bai, by: [0], remainder: true) @@ -36,7 +31,6 @@ workflow BAM_MARKDUPLICATES_PICARD { } BAM_STATS_SAMTOOLS ( ch_bam_bai, ch_fasta ) - ch_versions = ch_versions.mix(BAM_STATS_SAMTOOLS.out.versions) emit: bam = PICARD_MARKDUPLICATES.out.bam // channel: [ val(meta), path(bam) ] @@ -47,6 +41,4 @@ workflow BAM_MARKDUPLICATES_PICARD { stats = BAM_STATS_SAMTOOLS.out.stats // channel: [ val(meta), path(stats) ] flagstat = BAM_STATS_SAMTOOLS.out.flagstat // channel: [ val(meta), path(flagstat) ] idxstats = BAM_STATS_SAMTOOLS.out.idxstats // channel: [ val(meta), path(idxstats) ] - - versions = ch_versions // channel: [ versions.yml ] } diff --git a/subworkflows/nf-core/bam_rseqc/main.nf b/subworkflows/nf-core/bam_rseqc/main.nf index a698b30ab..d864a4a76 100644 --- a/subworkflows/nf-core/bam_rseqc/main.nf +++ b/subworkflows/nf-core/bam_rseqc/main.nf @@ -18,9 +18,6 @@ workflow BAM_RSEQC { rseqc_modules // list: rseqc modules to run main: - - ch_versions = Channel.empty() - ch_bam_bai .map { [ it[0], it[1] ] } .set { ch_bam } @@ -32,7 +29,6 @@ workflow BAM_RSEQC { if ('bam_stat' in rseqc_modules) { RSEQC_BAMSTAT ( ch_bam ) bamstat_txt = RSEQC_BAMSTAT.out.txt - ch_versions = ch_versions.mix(RSEQC_BAMSTAT.out.versions.first()) } // @@ -50,7 +46,6 @@ workflow BAM_RSEQC { innerdistance_mean = RSEQC_INNERDISTANCE.out.mean innerdistance_pdf = RSEQC_INNERDISTANCE.out.pdf innerdistance_rscript = RSEQC_INNERDISTANCE.out.rscript - ch_versions = ch_versions.mix(RSEQC_INNERDISTANCE.out.versions.first()) } // @@ -60,7 +55,6 @@ workflow BAM_RSEQC { if ('infer_experiment' in rseqc_modules) { RSEQC_INFEREXPERIMENT ( ch_bam, ch_bed ) inferexperiment_txt = RSEQC_INFEREXPERIMENT.out.txt - ch_versions = ch_versions.mix(RSEQC_INFEREXPERIMENT.out.versions.first()) } // @@ -82,7 +76,6 @@ workflow BAM_RSEQC { junctionannotation_events_pdf = RSEQC_JUNCTIONANNOTATION.out.events_pdf junctionannotation_rscript = RSEQC_JUNCTIONANNOTATION.out.rscript junctionannotation_log = RSEQC_JUNCTIONANNOTATION.out.log - ch_versions = ch_versions.mix(RSEQC_JUNCTIONANNOTATION.out.versions.first()) } // @@ -94,7 +87,6 @@ workflow BAM_RSEQC { RSEQC_JUNCTIONSATURATION ( ch_bam, ch_bed ) junctionsaturation_pdf = RSEQC_JUNCTIONSATURATION.out.pdf junctionsaturation_rscript = RSEQC_JUNCTIONSATURATION.out.rscript - ch_versions = ch_versions.mix(RSEQC_JUNCTIONSATURATION.out.versions.first()) } // @@ -104,7 +96,6 @@ workflow BAM_RSEQC { if ('read_distribution' in rseqc_modules) { RSEQC_READDISTRIBUTION ( ch_bam, ch_bed ) readdistribution_txt = RSEQC_READDISTRIBUTION.out.txt - ch_versions = ch_versions.mix(RSEQC_READDISTRIBUTION.out.versions.first()) } // @@ -120,7 +111,6 @@ workflow BAM_RSEQC { readduplication_pos_xls = RSEQC_READDUPLICATION.out.pos_xls readduplication_pdf = RSEQC_READDUPLICATION.out.pdf readduplication_rscript = RSEQC_READDUPLICATION.out.rscript - ch_versions = ch_versions.mix(RSEQC_READDUPLICATION.out.versions.first()) } // @@ -130,7 +120,6 @@ workflow BAM_RSEQC { if ('tin' in rseqc_modules) { RSEQC_TIN ( ch_bam_bai, ch_bed ) tin_txt = RSEQC_TIN.out.txt - ch_versions = ch_versions.mix(RSEQC_TIN.out.versions.first()) } emit: @@ -163,6 +152,4 @@ workflow BAM_RSEQC { readduplication_rscript // channel: [ val(meta), r ] tin_txt // channel: [ val(meta), txt ] - - versions = ch_versions // channel: [ versions.yml ] } diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/main.nf b/subworkflows/nf-core/bam_sort_stats_samtools/main.nf index fc1c652b9..42550a67e 100644 --- a/subworkflows/nf-core/bam_sort_stats_samtools/main.nf +++ b/subworkflows/nf-core/bam_sort_stats_samtools/main.nf @@ -12,14 +12,9 @@ workflow BAM_SORT_STATS_SAMTOOLS { ch_fasta // channel: [ val(meta), path(fasta) ] main: - - ch_versions = Channel.empty() - SAMTOOLS_SORT ( ch_bam ) - ch_versions = ch_versions.mix(SAMTOOLS_SORT.out.versions.first()) SAMTOOLS_INDEX ( SAMTOOLS_SORT.out.bam ) - ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first()) SAMTOOLS_SORT.out.bam .join(SAMTOOLS_INDEX.out.bai, by: [0], remainder: true) @@ -35,7 +30,6 @@ workflow BAM_SORT_STATS_SAMTOOLS { .set { ch_bam_bai } BAM_STATS_SAMTOOLS ( ch_bam_bai, ch_fasta ) - ch_versions = ch_versions.mix(BAM_STATS_SAMTOOLS.out.versions) emit: bam = SAMTOOLS_SORT.out.bam // channel: [ val(meta), [ bam ] ] @@ -45,6 +39,4 @@ workflow BAM_SORT_STATS_SAMTOOLS { stats = BAM_STATS_SAMTOOLS.out.stats // channel: [ val(meta), [ stats ] ] flagstat = BAM_STATS_SAMTOOLS.out.flagstat // channel: [ val(meta), [ flagstat ] ] idxstats = BAM_STATS_SAMTOOLS.out.idxstats // channel: [ val(meta), [ idxstats ] ] - - versions = ch_versions // channel: [ versions.yml ] } diff --git a/subworkflows/nf-core/bam_stats_samtools/main.nf b/subworkflows/nf-core/bam_stats_samtools/main.nf index 44d4c010a..34e8fe104 100644 --- a/subworkflows/nf-core/bam_stats_samtools/main.nf +++ b/subworkflows/nf-core/bam_stats_samtools/main.nf @@ -12,21 +12,14 @@ workflow BAM_STATS_SAMTOOLS { ch_fasta // channel: [ val(meta), path(fasta) ] main: - ch_versions = Channel.empty() - SAMTOOLS_STATS ( ch_bam_bai, ch_fasta ) - ch_versions = ch_versions.mix(SAMTOOLS_STATS.out.versions) SAMTOOLS_FLAGSTAT ( ch_bam_bai ) - ch_versions = ch_versions.mix(SAMTOOLS_FLAGSTAT.out.versions) SAMTOOLS_IDXSTATS ( ch_bam_bai ) - ch_versions = ch_versions.mix(SAMTOOLS_IDXSTATS.out.versions) emit: stats = SAMTOOLS_STATS.out.stats // channel: [ val(meta), path(stats) ] flagstat = SAMTOOLS_FLAGSTAT.out.flagstat // channel: [ val(meta), path(flagstat) ] idxstats = SAMTOOLS_IDXSTATS.out.idxstats // channel: [ val(meta), path(idxstats) ] - - versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/main.nf b/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/main.nf index 6c3b7b0cb..5cf7852d7 100644 --- a/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/main.nf +++ b/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/main.nf @@ -11,24 +11,17 @@ workflow BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG { sizes // path: chrom.sizes main: - - ch_versions = Channel.empty() - // // Clip bedGraph file // UCSC_BEDCLIP ( bedgraph, sizes ) - ch_versions = ch_versions.mix(UCSC_BEDCLIP.out.versions.first()) // // Convert bedGraph to bigWig // UCSC_BEDGRAPHTOBIGWIG ( UCSC_BEDCLIP.out.bedgraph, sizes ) - ch_versions = ch_versions.mix(UCSC_BEDGRAPHTOBIGWIG.out.versions.first()) emit: bigwig = UCSC_BEDGRAPHTOBIGWIG.out.bigwig // channel: [ val(meta), [ bigwig ] ] bedgraph = UCSC_BEDCLIP.out.bedgraph // channel: [ val(meta), [ bedgraph ] ] - - versions = ch_versions // channel: [ versions.yml ] } diff --git a/subworkflows/nf-core/fastq_align_hisat2/main.nf b/subworkflows/nf-core/fastq_align_hisat2/main.nf index a2ec1cf5e..4a24e1f63 100644 --- a/subworkflows/nf-core/fastq_align_hisat2/main.nf +++ b/subworkflows/nf-core/fastq_align_hisat2/main.nf @@ -11,20 +11,15 @@ workflow FASTQ_ALIGN_HISAT2 { main: - ch_versions = Channel.empty() - - // // Map reads with HISAT2 // HISAT2_ALIGN ( reads, index, splicesites ) - ch_versions = ch_versions.mix(HISAT2_ALIGN.out.versions.first()) // // Sort, index BAM file and run samtools stats, flagstat and idxstats // BAM_SORT_STATS_SAMTOOLS ( HISAT2_ALIGN.out.bam, ch_fasta ) - ch_versions = ch_versions.mix(BAM_SORT_STATS_SAMTOOLS.out.versions) emit: @@ -38,7 +33,5 @@ workflow FASTQ_ALIGN_HISAT2 { stats = BAM_SORT_STATS_SAMTOOLS.out.stats // channel: [ val(meta), [ stats ] ] flagstat = BAM_SORT_STATS_SAMTOOLS.out.flagstat // channel: [ val(meta), [ flagstat ] ] idxstats = BAM_SORT_STATS_SAMTOOLS.out.idxstats // channel: [ val(meta), [ idxstats ] ] - - versions = ch_versions // channel: [ versions.yml ] } diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf index 3dbb27eae..8b1f9048c 100644 --- a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf +++ b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf @@ -31,7 +31,6 @@ workflow FASTQ_FASTQC_UMITOOLS_FASTP { min_trimmed_reads // integer: > 0 main: - ch_versions = Channel.empty() fastqc_raw_html = Channel.empty() fastqc_raw_zip = Channel.empty() if (!skip_fastqc) { @@ -40,7 +39,6 @@ workflow FASTQ_FASTQC_UMITOOLS_FASTP { ) fastqc_raw_html = FASTQC_RAW.out.html fastqc_raw_zip = FASTQC_RAW.out.zip - ch_versions = ch_versions.mix(FASTQC_RAW.out.versions.first()) } umi_reads = reads @@ -51,7 +49,6 @@ workflow FASTQ_FASTQC_UMITOOLS_FASTP { ) umi_reads = UMITOOLS_EXTRACT.out.reads umi_log = UMITOOLS_EXTRACT.out.log - ch_versions = ch_versions.mix(UMITOOLS_EXTRACT.out.versions.first()) // Discard R1 / R2 if required if (umi_discard_read in [1,2]) { @@ -87,7 +84,6 @@ workflow FASTQ_FASTQC_UMITOOLS_FASTP { trim_log = FASTP.out.log trim_reads_fail = FASTP.out.reads_fail trim_reads_merged = FASTP.out.reads_merged - ch_versions = ch_versions.mix(FASTP.out.versions.first()) // // Filter FastQ files based on minimum trimmed read count after adapter trimming @@ -114,7 +110,6 @@ workflow FASTQ_FASTQC_UMITOOLS_FASTP { ) fastqc_trim_html = FASTQC_TRIM.out.html fastqc_trim_zip = FASTQC_TRIM.out.zip - ch_versions = ch_versions.mix(FASTQC_TRIM.out.versions.first()) } } @@ -135,6 +130,4 @@ workflow FASTQ_FASTQC_UMITOOLS_FASTP { fastqc_trim_html // channel: [ val(meta), [ html ] ] fastqc_trim_zip // channel: [ val(meta), [ zip ] ] - - versions = ch_versions.ifEmpty(null) // channel: [ versions.yml ] } diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf index db2e5b329..88f5a43c5 100644 --- a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf +++ b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf @@ -32,14 +32,12 @@ workflow FASTQ_FASTQC_UMITOOLS_TRIMGALORE { min_trimmed_reads // integer: > 0 main: - ch_versions = Channel.empty() fastqc_html = Channel.empty() fastqc_zip = Channel.empty() if (!skip_fastqc) { FASTQC (reads) fastqc_html = FASTQC.out.html fastqc_zip = FASTQC.out.zip - ch_versions = ch_versions.mix(FASTQC.out.versions.first()) } umi_reads = reads @@ -48,7 +46,6 @@ workflow FASTQ_FASTQC_UMITOOLS_TRIMGALORE { UMITOOLS_EXTRACT (reads) umi_reads = UMITOOLS_EXTRACT.out.reads umi_log = UMITOOLS_EXTRACT.out.log - ch_versions = ch_versions.mix(UMITOOLS_EXTRACT.out.versions.first()) // Discard R1 / R2 if required if (umi_discard_read in [1,2]) { @@ -75,7 +72,6 @@ workflow FASTQ_FASTQC_UMITOOLS_TRIMGALORE { trim_html = TRIMGALORE.out.html trim_zip = TRIMGALORE.out.zip trim_log = TRIMGALORE.out.log - ch_versions = ch_versions.mix(TRIMGALORE.out.versions.first()) // // Filter FastQ files based on minimum trimmed read count after adapter trimming @@ -118,6 +114,4 @@ workflow FASTQ_FASTQC_UMITOOLS_TRIMGALORE { trim_zip // channel: [ val(meta), [ zip ] ] trim_log // channel: [ val(meta), [ txt ] ] trim_read_count // channel: [ val(meta), val(count) ] - - versions = ch_versions.ifEmpty(null) // channel: [ versions.yml ] } diff --git a/subworkflows/nf-core/fastq_subsample_fq_salmon/main.nf b/subworkflows/nf-core/fastq_subsample_fq_salmon/main.nf index 0ac3e53a3..089546322 100644 --- a/subworkflows/nf-core/fastq_subsample_fq_salmon/main.nf +++ b/subworkflows/nf-core/fastq_subsample_fq_salmon/main.nf @@ -17,22 +17,17 @@ workflow FASTQ_SUBSAMPLE_FQ_SALMON { make_index // boolean: Whether to create salmon index before running salmon quant main: - - ch_versions = Channel.empty() - // // Create Salmon index if required // if (make_index) { ch_index = SALMON_INDEX ( ch_genome_fasta, ch_transcript_fasta ).index - ch_versions = ch_versions.mix(SALMON_INDEX.out.versions) } // // Sub-sample FastQ files with fq // FQ_SUBSAMPLE ( ch_reads ) - ch_versions = ch_versions.mix(FQ_SUBSAMPLE.out.versions.first()) // // Pseudo-alignment with Salmon @@ -40,7 +35,6 @@ workflow FASTQ_SUBSAMPLE_FQ_SALMON { def lib_type = 'A' def alignment_mode = false SALMON_QUANT ( FQ_SUBSAMPLE.out.fastq, ch_index, ch_gtf, ch_transcript_fasta, alignment_mode, lib_type ) - ch_versions = ch_versions.mix(SALMON_QUANT.out.versions.first()) emit: index = ch_index // channel: [ index ] @@ -49,6 +43,4 @@ workflow FASTQ_SUBSAMPLE_FQ_SALMON { results = SALMON_QUANT.out.results // channel: [ val(meta), results_dir ] json_info = SALMON_QUANT.out.json_info // channel: [ val(meta), json_info - - versions = ch_versions // channel: [ versions.yml ] } diff --git a/workflows/rnaseq.nf b/workflows/rnaseq.nf index 955a727c3..fbe30cc7d 100755 --- a/workflows/rnaseq.nf +++ b/workflows/rnaseq.nf @@ -151,8 +151,6 @@ def pass_strand_check = [:] workflow RNASEQ { - ch_versions = Channel.empty() - // // SUBWORKFLOW: Uncompress and prepare reference genome files // @@ -176,7 +174,6 @@ workflow RNASEQ { biotype, prepareToolIndices ) - ch_versions = ch_versions.mix(PREPARE_GENOME.out.versions) // Check if contigs in genome fasta file > 512 Mbp if (!params.skip_alignment && !params.bam_csi_index) { @@ -221,7 +218,6 @@ workflow RNASEQ { .reads .mix(ch_fastq.single) .set { ch_cat_fastq } - ch_versions = ch_versions.mix(CAT_FASTQ.out.versions.first().ifEmpty(null)) // Branch FastQ channels if 'auto' specified to infer strandedness ch_cat_fastq @@ -252,7 +248,6 @@ workflow RNASEQ { PREPARE_GENOME.out.salmon_index, !params.salmon_index && !('salmon' in prepareToolIndices) ) - ch_versions = ch_versions.mix(FASTQ_SUBSAMPLE_FQ_SALMON.out.versions) FASTQ_SUBSAMPLE_FQ_SALMON .out @@ -287,7 +282,6 @@ workflow RNASEQ { ch_fastqc_trim_multiqc = FASTQ_FASTQC_UMITOOLS_TRIMGALORE.out.trim_zip ch_trim_log_multiqc = FASTQ_FASTQC_UMITOOLS_TRIMGALORE.out.trim_log ch_trim_read_count = FASTQ_FASTQC_UMITOOLS_TRIMGALORE.out.trim_read_count - ch_versions = ch_versions.mix(FASTQ_FASTQC_UMITOOLS_TRIMGALORE.out.versions) } // @@ -311,7 +305,6 @@ workflow RNASEQ { ch_fastqc_trim_multiqc = FASTQ_FASTQC_UMITOOLS_FASTP.out.fastqc_trim_zip ch_trim_log_multiqc = FASTQ_FASTQC_UMITOOLS_FASTP.out.trim_json ch_trim_read_count = FASTQ_FASTQC_UMITOOLS_FASTP.out.trim_read_count - ch_versions = ch_versions.mix(FASTQ_FASTQC_UMITOOLS_FASTP.out.versions) } // @@ -347,7 +340,6 @@ workflow RNASEQ { ) .primary_fastq .set { ch_filtered_reads } - ch_versions = ch_versions.mix(BBMAP_BBSPLIT.out.versions.first()) } // @@ -365,7 +357,6 @@ workflow RNASEQ { .set { ch_filtered_reads } ch_sortmerna_multiqc = SORTMERNA.out.log - ch_versions = ch_versions.mix(SORTMERNA.out.versions.first()) } // @@ -400,7 +391,6 @@ workflow RNASEQ { if (params.bam_csi_index) { ch_genome_bam_index = ALIGN_STAR.out.csi } - ch_versions = ch_versions.mix(ALIGN_STAR.out.versions) // // SUBWORKFLOW: Remove duplicate reads from BAM file based on UMIs @@ -419,7 +409,6 @@ workflow RNASEQ { if (params.bam_csi_index) { ch_genome_bam_index = BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.csi } - ch_versions = ch_versions.mix(BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.versions) // Co-ordinate sort, index and run stats on transcriptome BAM BAM_SORT_STATS_SAMTOOLS ( @@ -458,7 +447,6 @@ workflow RNASEQ { UMITOOLS_PREPAREFORSALMON ( ch_umitools_dedup_bam.paired_end ) - ch_versions = ch_versions.mix(UMITOOLS_PREPAREFORSALMON.out.versions.first()) ch_umitools_dedup_bam .single_end @@ -477,7 +465,6 @@ workflow RNASEQ { true, params.salmon_quant_libtype ?: '' ) - ch_versions = ch_versions.mix(QUANTIFY_STAR_SALMON.out.versions) if (!params.skip_qc & !params.skip_deseq2_qc) { DESEQ2_QC_STAR_SALMON ( @@ -487,7 +474,6 @@ workflow RNASEQ { ) ch_aligner_pca_multiqc = DESEQ2_QC_STAR_SALMON.out.pca_multiqc ch_aligner_clustering_multiqc = DESEQ2_QC_STAR_SALMON.out.dists_multiqc - ch_versions = ch_versions.mix(DESEQ2_QC_STAR_SALMON.out.versions) } } @@ -511,7 +497,6 @@ workflow RNASEQ { if (params.bam_csi_index) { ch_genome_bam_index = QUANTIFY_RSEM.out.csi } - ch_versions = ch_versions.mix(QUANTIFY_RSEM.out.versions) if (!params.skip_qc & !params.skip_deseq2_qc) { DESEQ2_QC_RSEM ( @@ -521,7 +506,6 @@ workflow RNASEQ { ) ch_aligner_pca_multiqc = DESEQ2_QC_RSEM.out.pca_multiqc ch_aligner_clustering_multiqc = DESEQ2_QC_RSEM.out.dists_multiqc - ch_versions = ch_versions.mix(DESEQ2_QC_RSEM.out.versions) } } @@ -545,7 +529,6 @@ workflow RNASEQ { if (params.bam_csi_index) { ch_genome_bam_index = FASTQ_ALIGN_HISAT2.out.csi } - ch_versions = ch_versions.mix(FASTQ_ALIGN_HISAT2.out.versions) // // SUBWORKFLOW: Remove duplicate reads from BAM file based on UMIs @@ -563,7 +546,6 @@ workflow RNASEQ { if (params.bam_csi_index) { ch_genome_bam_index = BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.csi } - ch_versions = ch_versions.mix(BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.versions) } } @@ -617,7 +599,6 @@ workflow RNASEQ { ch_genome_bam ) ch_preseq_multiqc = PRESEQ_LCEXTRAP.out.lc_extrap - ch_versions = ch_versions.mix(PRESEQ_LCEXTRAP.out.versions.first()) } // @@ -639,7 +620,6 @@ workflow RNASEQ { if (params.bam_csi_index) { ch_genome_bam_index = BAM_MARKDUPLICATES_PICARD.out.csi } - ch_versions = ch_versions.mix(BAM_MARKDUPLICATES_PICARD.out.versions) } // @@ -650,7 +630,6 @@ workflow RNASEQ { ch_genome_bam, PREPARE_GENOME.out.gtf ) - ch_versions = ch_versions.mix(STRINGTIE_STRINGTIE.out.versions.first()) } // @@ -676,14 +655,12 @@ workflow RNASEQ { SUBREAD_FEATURECOUNTS ( ch_featurecounts ) - ch_versions = ch_versions.mix(SUBREAD_FEATURECOUNTS.out.versions.first()) MULTIQC_CUSTOM_BIOTYPE ( SUBREAD_FEATURECOUNTS.out.counts, ch_biotypes_header_multiqc ) ch_featurecounts_multiqc = MULTIQC_CUSTOM_BIOTYPE.out.tsv - ch_versions = ch_versions.mix(MULTIQC_CUSTOM_BIOTYPE.out.versions.first()) } // @@ -694,7 +671,6 @@ workflow RNASEQ { BEDTOOLS_GENOMECOV ( ch_genome_bam ) - ch_versions = ch_versions.mix(BEDTOOLS_GENOMECOV.out.versions.first()) // // SUBWORKFLOW: Convert bedGraph to bigWig @@ -703,7 +679,6 @@ workflow RNASEQ { BEDTOOLS_GENOMECOV.out.bedgraph_forward, PREPARE_GENOME.out.chrom_sizes ) - ch_versions = ch_versions.mix(BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD.out.versions) BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE ( BEDTOOLS_GENOMECOV.out.bedgraph_reverse, @@ -732,7 +707,6 @@ workflow RNASEQ { PREPARE_GENOME.out.gtf.map { [ [:], it ] } ) ch_qualimap_multiqc = QUALIMAP_RNASEQ.out.results - ch_versions = ch_versions.mix(QUALIMAP_RNASEQ.out.versions.first()) } if (!params.skip_dupradar) { @@ -741,7 +715,6 @@ workflow RNASEQ { PREPARE_GENOME.out.gtf ) ch_dupradar_multiqc = DUPRADAR.out.multiqc - ch_versions = ch_versions.mix(DUPRADAR.out.versions.first()) } if (!params.skip_rseqc && rseqc_modules.size() > 0) { @@ -758,7 +731,6 @@ workflow RNASEQ { ch_readdistribution_multiqc = BAM_RSEQC.out.readdistribution_txt ch_readduplication_multiqc = BAM_RSEQC.out.readduplication_pos_xls ch_tin_multiqc = BAM_RSEQC.out.tin_txt - ch_versions = ch_versions.mix(BAM_RSEQC.out.versions) ch_inferexperiment_multiqc .map { @@ -803,7 +775,6 @@ workflow RNASEQ { params.salmon_quant_libtype ?: '' ) ch_salmon_multiqc = QUANTIFY_SALMON.out.results - ch_versions = ch_versions.mix(QUANTIFY_SALMON.out.versions) if (!params.skip_qc & !params.skip_deseq2_qc) { DESEQ2_QC_SALMON ( @@ -813,7 +784,6 @@ workflow RNASEQ { ) ch_pseudoaligner_pca_multiqc = DESEQ2_QC_SALMON.out.pca_multiqc ch_pseudoaligner_clustering_multiqc = DESEQ2_QC_SALMON.out.dists_multiqc - ch_versions = ch_versions.mix(DESEQ2_QC_SALMON.out.versions) } } @@ -821,7 +791,7 @@ workflow RNASEQ { // MODULE: Pipeline reporting // CUSTOM_DUMPSOFTWAREVERSIONS ( - ch_versions.unique().collectFile(name: 'collated_versions.yml') + Channel.topic('versions').unique().collectFile(name: 'collated_versions.yml') ) //