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| workflow_id: https://raw.githubusercontent.com/molgenis/vip/compatibility%2Fwfexs/vip_vcf.nf | ||
| workflow_config: | ||
| secure: false | ||
| containerType: none | ||
| nextflow: | ||
| version: 21.10.6 | ||
| # All the inputs must be URLs or CURIEs from identifiers.org | ||
| placeholders: | ||
| assembly: "GRCh37" | ||
| annotate_ver: 20230116 | ||
| resources_prefix: file:///scratch/laura/vip/resources | ||
| singularity_image_dir: file:///scratch/laura/vip/images | ||
| //public_resources_prefix: https://download.molgeniscloud.org/downloads/vip/resources | ||
| params: | ||
| // assembly: "{assembly}" | ||
| input: | ||
| c-l-a-s-s: File | ||
| url: file:///scratch/laura/vip/FAM0001816_subset_v2.vcf.gz | ||
| secondary-urls: file:///scratch/laura/vip/FAM0001815_subset_v2.vcf.gz.tbi | ||
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| GRCh37.reference.fasta: | ||
| c-l-a-s-s: File | ||
| url: "{resources_prefix}/GRCh37/human_g1k_v37.fasta.gz" | ||
| GRCh37.reference.fastaFai: | ||
| c-l-a-s-s: File | ||
| url: "{resources_prefix}/GRCh37/human_g1k_v37.fasta.gz.fai" | ||
| GRCh37.reference.fastaGzi: | ||
| c-l-a-s-s: File | ||
| url: "{resources_prefix}/GRCh37/human_g1k_v37.fasta.gz.gzi" | ||
|
|
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| vcf.gvcf_merge_preset: "gatk" | ||
| vcf.start: "" | ||
| vcf.annotate.annotsv_cache_dir: | ||
| c-l-a-s-s: Directory | ||
| url: "{resources_prefix}/annotsv/v3.2.3" | ||
| vcf.annotate.vep_buffer_size: 1000 | ||
| vcf.annotate.vep_cache_dir: | ||
| c-l-a-s-s: Directory | ||
| url: "{resources_prefix}/vep/cache" | ||
| vcf.annotate.vep_plugin_dir: | ||
| c-l-a-s-s: Directory | ||
| url: "{resources_prefix}/vep/plugins" | ||
| vcf.annotate.vep_plugin_hpo: | ||
| c-l-a-s-s: File | ||
| url: "{resources_prefix}/hpo_{annotate_ver}.tsv" | ||
| vcf.annotate.vep_plugin_inheritance: | ||
| c-l-a-s-s: File | ||
| url: "{resources_prefix}/inheritance_{annotate_ver}.tsv" | ||
| vcf.annotate.vep_plugin_vkgl_mode: 1 | ||
| vcf.annotate.GRCh37.capice_model: | ||
| c-l-a-s-s: File | ||
| url: "{resources_prefix}/GRCh37/capice_model_v5.0.0-v1.ubj" | ||
| vcf.annotate.GRCh37.vep_custom_gnomad: | ||
| c-l-a-s-s: File | ||
| url: "{resources_prefix}/GRCh37/gnomad.total.r2.1.1.sites.stripped.patch1.vcf.gz" | ||
| vcf.annotate.GRCh37.vep_custom_clinvar: | ||
| c-l-a-s-s: File | ||
| url: "{resources_prefix}/GRCh37/clinvar_20230115.vcf.gz" | ||
| vcf.annotate.GRCh37.vep_custom_phylop: | ||
| c-l-a-s-s: File | ||
| url: "{resources_prefix}/GRCh37/hg19.100way.phyloP100way.bw" | ||
| vcf.annotate.GRCh37.vep_plugin_spliceai_indel: | ||
| c-l-a-s-s: File | ||
| url: "{resources_prefix}/GRCh37/spliceai_scores.masked.indel.hg19.vcf.gz" | ||
| vcf.annotate.GRCh37.vep_plugin_spliceai_snv: | ||
| c-l-a-s-s: File | ||
| url: "{resources_prefix}/GRCh37/spliceai_scores.masked.snv.hg19.vcf.gz" | ||
| vcf.annotate.GRCh37.vep_plugin_utrannotator: | ||
| c-l-a-s-s: File | ||
| url: "{resources_prefix}/GRCh37/uORF_5UTR_PUBLIC.txt" | ||
| vcf.annotate.GRCh37.vep_plugin_vkgl: | ||
| c-l-a-s-s: File | ||
| url: "{resources_prefix}/GRCh37/vkgl_consensus_20230101.tsv" | ||
| vcf.classify.annotate_labels: 0 | ||
| vcf.classify.annotate_path: 1 | ||
| vcf.classify.GRCh37.decision_tree: | ||
| c-l-a-s-s: File | ||
| url: "{resources_prefix}/decision_tree_{assembly}.json" | ||
| vcf.classify_samples.annotate_labels: 0 | ||
| vcf.classify_samples.annotate_path: 1 | ||
| vcf.classify_samples.GRCh37.decision_tree: | ||
| c-l-a-s-s: File | ||
| url: "{resources_prefix}/decision_tree_samples.json" | ||
| vcf.filter.classes: "VUS,LP,P" | ||
| vcf.filter.consequences: true | ||
| vcf.filter_samples.classes: "MV,OK" | ||
| vcf.report.max_records: "" | ||
| vcf.report.max_samples: "" | ||
| vcf.report.template: "" | ||
| vcf.report.GRCh37.genes: | ||
| c-l-a-s-s: File | ||
| url: "{resources_prefix}/GRCh37/GCF_000001405.25_GRCh37.p13_genomic_g1k.gff.gz" | ||
|
|
||
| CMD_ANNOTSV: "singularity exec --bind {singularity_image_dir} {singularity_image_dir}/annotsv-3.2.3.sif AnnotSV" | ||
| CMD_BCFTOOLS: "singularity exec --bind {singularity_image_dir} {singularity_image_dir}/bcftools-1.14.sif bcftools" | ||
| CMD_CAPICE: "singularity exec --bind {singularity_image_dir} {singularity_image_dir}/capice-5.1.0.sif capice" | ||
| CMD_GLNEXUS: "singularity exec --bind {singularity_image_dir} {singularity_image_dir}/glnexus_v1.4.1.sif glnexus_cli" | ||
| CMD_VEP: "singularity exec --bind {singularity_image_dir} {singularity_image_dir}/vep-107.0.sif vep" | ||
| CMD_FILTERVEP: "singularity exec --bind {singularity_image_dir} {singularity_image_dir}/vep-107.0.sif filter_vep" | ||
| CMD_BGZIP: "singularity exec --bind {singularity_image_dir} {singularity_image_dir}/vep-107.0.sif bgzip" | ||
| CMD_SAMTOOLS: "singularity exec --bind {singularity_image_dir} {singularity_image_dir}/samtools-1.16.sif samtools" | ||
| CMD_VCFREPORT: "singularity exec --bind {singularity_image_dir} {singularity_image_dir}/vcf-report-5.2.1.sif" | ||
| CMD_VCFDECISIONTREE: "singularity exec --bind {singularity_image_dir} {singularity_image_dir}/vcf-decision-tree-3.5.2.sif" | ||
| CMD_VCFINHERITANCEMATCHER: "singularity exec --bind {singularity_image_dir} {singularity_image_dir}/vcf-inheritance-matcher-2.1.5.sif" | ||
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| output: | ||
| c-l-a-s-s: Directory | ||
| autoFill: true | ||
| autoPrefix: true | ||
|
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||
| outputs: | ||
| output: | ||
| c-l-a-s-s: Directory | ||
| glob: "*" |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,114 @@ | ||
| workflow_id: https://raw.githubusercontent.com/molgenis/vip/compatibility%2Fwfexs/vip_vcf.nf | ||
| workflow_config: | ||
| secure: false | ||
| containerType: none | ||
| nextflow: | ||
| version: 21.10.6 | ||
| # All the inputs must be URLs or CURIEs from identifiers.org | ||
| placeholders: | ||
| assembly: "GRCh37" | ||
| annotate_ver: 20230116 | ||
| resources_prefix: file:///scratch/laura/vip/resources | ||
| singularity_image_dir: file:///scratch/laura/vip/images | ||
| //public_resources_prefix: https://download.molgeniscloud.org/downloads/vip/resources | ||
| params: | ||
| // assembly: "{assembly}" | ||
| input: | ||
| c-l-a-s-s: File | ||
| url: file:///scratch/laura/vip/FAM0001816_subset_v2.vcf.gz | ||
| secondary-urls: file:///scratch/laura/vip/FAM0001815_subset_v2.vcf.gz.tbi | ||
|
|
||
| GRCh37.reference.fasta: | ||
| c-l-a-s-s: File | ||
| url: "{resources_prefix}/GRCh37/human_g1k_v37.fasta.gz" | ||
| GRCh37.reference.fastaFai: | ||
| c-l-a-s-s: File | ||
| url: "{resources_prefix}/GRCh37/human_g1k_v37.fasta.gz.fai" | ||
| GRCh37.reference.fastaGzi: | ||
| c-l-a-s-s: File | ||
| url: "{resources_prefix}/GRCh37/human_g1k_v37.fasta.gz.gzi" | ||
|
|
||
| vcf.gvcf_merge_preset: "gatk" | ||
| vcf.start: "" | ||
| vcf.annotate.annotsv_cache_dir: | ||
| c-l-a-s-s: Directory | ||
| url: "{resources_prefix}/annotsv/v3.2.3" | ||
| vcf.annotate.vep_buffer_size: 1000 | ||
| vcf.annotate.vep_cache_dir: | ||
| c-l-a-s-s: Directory | ||
| url: "{resources_prefix}/vep/cache" | ||
| vcf.annotate.vep_plugin_dir: | ||
| c-l-a-s-s: Directory | ||
| url: "{resources_prefix}/vep/plugins" | ||
| vcf.annotate.vep_plugin_hpo: | ||
| c-l-a-s-s: File | ||
| url: "{resources_prefix}/hpo_{annotate_ver}.tsv" | ||
| vcf.annotate.vep_plugin_inheritance: | ||
| c-l-a-s-s: File | ||
| url: "{resources_prefix}/inheritance_{annotate_ver}.tsv" | ||
| vcf.annotate.vep_plugin_vkgl_mode: 1 | ||
| vcf.annotate.GRCh37.capice_model: | ||
| c-l-a-s-s: File | ||
| url: "{resources_prefix}/GRCh37/capice_model_v5.0.0-v1.ubj" | ||
| vcf.annotate.GRCh37.vep_custom_gnomad: | ||
| c-l-a-s-s: File | ||
| url: "{resources_prefix}/GRCh37/gnomad.total.r2.1.1.sites.stripped.patch1.vcf.gz" | ||
| vcf.annotate.GRCh37.vep_custom_clinvar: | ||
| c-l-a-s-s: File | ||
| url: "{resources_prefix}/GRCh37/clinvar_20230115.vcf.gz" | ||
| vcf.annotate.GRCh37.vep_custom_phylop: | ||
| c-l-a-s-s: File | ||
| url: "{resources_prefix}/GRCh37/hg19.100way.phyloP100way.bw" | ||
| vcf.annotate.GRCh37.vep_plugin_spliceai_indel: | ||
| c-l-a-s-s: File | ||
| url: "{resources_prefix}/GRCh37/spliceai_scores.masked.indel.hg19.vcf.gz" | ||
| vcf.annotate.GRCh37.vep_plugin_spliceai_snv: | ||
| c-l-a-s-s: File | ||
| url: "{resources_prefix}/GRCh37/spliceai_scores.masked.snv.hg19.vcf.gz" | ||
| vcf.annotate.GRCh37.vep_plugin_utrannotator: | ||
| c-l-a-s-s: File | ||
| url: "{resources_prefix}/GRCh37/uORF_5UTR_PUBLIC.txt" | ||
| vcf.annotate.GRCh37.vep_plugin_vkgl: | ||
| c-l-a-s-s: File | ||
| url: "{resources_prefix}/GRCh37/vkgl_consensus_20230101.tsv" | ||
| vcf.classify.annotate_labels: 0 | ||
| vcf.classify.annotate_path: 1 | ||
| vcf.classify.GRCh37.decision_tree: | ||
| c-l-a-s-s: File | ||
| url: "{resources_prefix}/decision_tree_{assembly}.json" | ||
| vcf.classify_samples.annotate_labels: 0 | ||
| vcf.classify_samples.annotate_path: 1 | ||
| vcf.classify_samples.GRCh37.decision_tree: | ||
| c-l-a-s-s: File | ||
| url: "{resources_prefix}/decision_tree_samples.json" | ||
| vcf.filter.classes: "VUS,LP,P" | ||
| vcf.filter.consequences: true | ||
| vcf.filter_samples.classes: "MV,OK" | ||
| vcf.report.max_records: "" | ||
| vcf.report.max_samples: "" | ||
| vcf.report.template: "" | ||
| vcf.report.GRCh37.genes: | ||
| c-l-a-s-s: File | ||
| url: "{resources_prefix}/GRCh37/GCF_000001405.25_GRCh37.p13_genomic_g1k.gff.gz" | ||
|
|
||
| CMD_ANNOTSV: "singularity exec --bind {singularity_image_dir} {singularity_image_dir}/annotsv-3.2.3.sif AnnotSV" | ||
| CMD_BCFTOOLS: "singularity exec --bind {singularity_image_dir} {singularity_image_dir}/bcftools-1.14.sif bcftools" | ||
| CMD_CAPICE: "singularity exec --bind {singularity_image_dir} {singularity_image_dir}/capice-5.1.0.sif capice" | ||
| CMD_GLNEXUS: "singularity exec --bind {singularity_image_dir} {singularity_image_dir}/glnexus_v1.4.1.sif glnexus_cli" | ||
| CMD_VEP: "singularity exec --bind {singularity_image_dir} {singularity_image_dir}/vep-107.0.sif vep" | ||
| CMD_FILTERVEP: "singularity exec --bind {singularity_image_dir} {singularity_image_dir}/vep-107.0.sif filter_vep" | ||
| CMD_BGZIP: "singularity exec --bind {singularity_image_dir} {singularity_image_dir}/vep-107.0.sif bgzip" | ||
| CMD_SAMTOOLS: "singularity exec --bind {singularity_image_dir} {singularity_image_dir}/samtools-1.16.sif samtools" | ||
| CMD_VCFREPORT: "singularity exec --bind {singularity_image_dir} {singularity_image_dir}/vcf-report-5.2.1.sif" | ||
| CMD_VCFDECISIONTREE: "singularity exec --bind {singularity_image_dir} {singularity_image_dir}/vcf-decision-tree-3.5.2.sif" | ||
| CMD_VCFINHERITANCEMATCHER: "singularity exec --bind {singularity_image_dir} {singularity_image_dir}/vcf-inheritance-matcher-2.1.5.sif" | ||
|
|
||
| output: | ||
| c-l-a-s-s: Directory | ||
| autoFill: true | ||
| autoPrefix: true | ||
|
|
||
| outputs: | ||
| output: | ||
| c-l-a-s-s: Directory | ||
| glob: "*" |