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Structured config files into sub-folders for easy access. Removed red…
…undant code and moved subworkflows to correspondent folders. Fixes in rnadnavar.nf workflow and input check. Removed dependency in schema_input.json for lane. Added modules and subwrokflows the proper way.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,87 @@ | ||
| /* | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| Config file for defining DSL2 per module options and publishing paths | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| Available keys to override module options: | ||
| ext.args = Additional arguments appended to command in module. | ||
| ext.args2 = Second set of arguments appended to command in module (multi-tool modules). | ||
| ext.args3 = Third set of arguments appended to command in module (multi-tool modules). | ||
| ext.prefix = File name prefix for output files. | ||
| ext.when = When to run the module. | ||
| ---------------------------------------------------------------------------------------- | ||
| */ | ||
|
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| // BAM TO FASTQ | ||
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| process { // alignment_to_fastq | ||
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| withName: 'COLLATE_FASTQ_MAP' { | ||
| ext.args2 = '-N' | ||
| ext.prefix = {"${meta.id}.mapped"} | ||
| publishDir = [ | ||
| //specify to avoid publishing, overwritten otherwise | ||
| enabled: false | ||
| ] | ||
| } | ||
|
|
||
| withName: 'COLLATE_FASTQ_UNMAP' { | ||
| ext.args2 = '-N' | ||
| ext.prefix = {"${meta.id}.unmapped"} | ||
| publishDir = [ | ||
| //specify to avoid publishing, overwritten otherwise | ||
| enabled: false | ||
| ] | ||
| } | ||
|
|
||
| withName: 'SAMTOOLS_VIEW_MAP_MAP' { | ||
| ext.args = '-b -f1 -F12' | ||
| ext.prefix = {"${meta.id}.map_map"} | ||
| publishDir = [ | ||
| //specify to avoid publishing, overwritten otherwise | ||
| enabled: false | ||
| ] | ||
| } | ||
|
|
||
| withName: 'SAMTOOLS_VIEW_MAP_UNMAP' { | ||
| ext.args = '-b -f8 -F260' | ||
| ext.prefix = {"${meta.id}.map_unmap"} | ||
| publishDir = [ | ||
| //specify to avoid publishing, overwritten otherwise | ||
| enabled: false | ||
| ] | ||
| } | ||
|
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||
| withName: 'SAMTOOLS_VIEW_UNMAP_MAP' { | ||
| ext.args = '-b -f4 -F264' | ||
| ext.prefix = {"${meta.id}.unmap_map"} | ||
| publishDir = [ | ||
| //specify to avoid publishing, overwritten otherwise | ||
| enabled: false | ||
| ] | ||
| } | ||
|
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||
| withName: 'SAMTOOLS_VIEW_UNMAP_UNMAP' { | ||
| ext.args = '-b -f12 -F256' | ||
| ext.prefix = {"${meta.id}.unmap_unmap"} | ||
| publishDir = [ | ||
| //specify to avoid publishing, overwritten otherwise | ||
| enabled: false | ||
| ] | ||
| } | ||
|
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||
| withName: 'SAMTOOLS_MERGE_UNMAP' { | ||
| ext.prefix = {"${meta.id}.merged_unmap"} | ||
| publishDir = [ | ||
| //specify to avoid publishing, overwritten otherwise | ||
| enabled: false | ||
| ] | ||
| } | ||
| withName: 'CAT_FASTQ' { | ||
| publishDir = [ | ||
| enabled: params.save_split_fastqs, | ||
| mode: params.publish_dir_mode, | ||
| path: { "${params.outdir}/reference/bed" }, | ||
| saveAs: { filename -> filename.equals('versions.yml') ? null : filename } | ||
| ] | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,69 @@ | ||
| /* | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| Config file for defining DSL2 per module options and publishing paths | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| Available keys to override module options: | ||
| ext.args = Additional arguments appended to command in module. | ||
| ext.args2 = Second set of arguments appended to command in module (multi-tool modules). | ||
| ext.args3 = Third set of arguments appended to command in module (multi-tool modules). | ||
| ext.prefix = File name prefix for output files. | ||
| ext.when = When to run the module. | ||
| ---------------------------------------------------------------------------------------- | ||
| */ | ||
|
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||
| // ANNOTATE | ||
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| process { // annotate | ||
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| // VEP TODO: is vep_custom_args working?? | ||
| if (params.tools && params.tools.split(',').contains('vep')) { | ||
| withName: 'ENSEMBLVEP_VEP' { | ||
| ext.args = { [ | ||
| (params.vep_dbnsfp && params.dbnsfp && !params.dbnsfp_consequence) ? "--plugin dbNSFP,${params.dbnsfp.split("/")[-1]},${params.dbnsfp_fields}" : '', | ||
| (params.vep_dbnsfp && params.dbnsfp && params.dbnsfp_consequence) ? "--plugin dbNSFP,'consequence=${params.dbnsfp_consequence}',${params.dbnsfp.split("/")[-1]},${params.dbnsfp_fields}" : '', | ||
| (params.vep_loftee) ? "--plugin LoF,loftee_path:/opt/conda/envs/nf-core-vep-${params.vep_version}/share/ensembl-vep-${params.vep_version}-0" : '', | ||
| (params.vep_spliceai && params.spliceai_snv && params.spliceai_indel) ? "--plugin SpliceAI,snv=${params.spliceai_snv.split("/")[-1]},indel=${params.spliceai_indel.split("/")[-1]}" : '', | ||
| (params.vep_spliceregion) ? '--plugin SpliceRegion' : '', | ||
| (params.vep_out_format) ? "--${params.vep_out_format}" : '--vcf', | ||
| (params.vep_custom_args) ?: '' | ||
| ].join(' ').trim() } | ||
| // If just VEP: <vcf prefix>_VEP.ann.vcf | ||
| ext.prefix = { vcf.baseName - ".vcf" + "_VEP.ann" } | ||
| publishDir = [ | ||
| [ | ||
| mode: params.publish_dir_mode, | ||
| path: { "${params.outdir}/reports/EnsemblVEP/${meta.variantcaller}/${meta.id}/" }, | ||
| pattern: "*html" | ||
| ], | ||
| [ | ||
| mode: params.publish_dir_mode, | ||
| path: { "${params.outdir}/annotation/${meta.variantcaller}/${meta.id}/" }, | ||
| pattern: "*{gz}" | ||
| ] | ||
| ] | ||
| } | ||
| } | ||
|
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| // ALL ANNOTATION TOOLS | ||
| if (params.tools && (params.tools.split(',').contains('snpeff') || params.tools.split(',').contains('vep') || params.tools.split(',').contains('merge'))) { | ||
| withName: "NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:.*:(TABIX_BGZIPTABIX|TABIX_TABIX)" { | ||
| ext.prefix = { input.name - ".vcf" } | ||
| publishDir = [ | ||
| mode: params.publish_dir_mode, | ||
| path: { "${params.outdir}/annotation/${meta.variantcaller}/${meta.id}/" }, | ||
| pattern: "*{gz.tbi}" | ||
| ] | ||
| } | ||
| } | ||
|
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| if (params.tools && (params.tools.split(',').contains('snpeff') || params.tools.split(',').contains('merge'))) { | ||
| withName: 'NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX' { | ||
| publishDir = [ | ||
| mode: params.publish_dir_mode, | ||
| path: { "${params.outdir}/annotation/${meta.variantcaller}/${meta.id}/" }, | ||
| pattern: "*{gz,gz.tbi}", | ||
| saveAs: { params.tools.split(',').contains('snpeff') ? it : null } | ||
| ] | ||
| } | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,58 @@ | ||
| /* | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| Config file for defining DSL2 per module options and publishing paths | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| Available keys to override module options: | ||
| ext.args = Additional arguments appended to command in module. | ||
| ext.args2 = Second set of arguments appended to command in module (multi-tool modules). | ||
| ext.args3 = Third set of arguments appended to command in module (multi-tool modules). | ||
| ext.prefix = File name prefix for output files. | ||
| ext.when = When to run the module. | ||
| ---------------------------------------------------------------------------------------- | ||
| */ | ||
|
|
||
| // NORMALISE | ||
|
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| process { // normalise | ||
|
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| if (params.skip_toos && params.skip_toos.split(',').contains('normalise')) { | ||
| // VT | ||
| // TODO: stats are not going to the report dir - no idea why | ||
| withName: 'VT_DECOMPOSE'{ | ||
| ext.args = "" | ||
| ext.prefix = { "${vcf.baseName.minus(".vcf")}.dec" } | ||
| publishDir = [ | ||
| [ | ||
| mode: params.publish_dir_mode, | ||
| path: { "${params.outdir}/reports/vt/" }, | ||
| pattern: {'*dec.stats'}, | ||
| saveAs: {"${meta.variantcaller}/${meta.patient}/${meta.id}/${it}"}, | ||
| enabled: true | ||
| ], | ||
| [ | ||
| mode: params.publish_dir_mode, | ||
| path: { "${params.outdir}/variant_calling/" }, | ||
| pattern: {"*{vcf.gz,vcf.gz.tbi}"}, | ||
| saveAs: {"${meta.variantcaller}/${meta.patient}/${meta.id}/${it}"}, | ||
| enabled: false // store normalised results only | ||
| ] | ||
| ] | ||
| } | ||
|
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| withName: 'VT_NORMALIZE'{ | ||
| ext.args = {"-n"} | ||
| ext.prefix = { "${vcf.baseName.minus(".dec.vcf")}.norm" } | ||
| publishDir = [[ | ||
| path: { "${params.outdir}/variant_calling/" }, | ||
| pattern: "*{vcf.gz,vcf.gz.tbi,norm.stats}", | ||
| saveAs: { "${meta.variantcaller}/${meta.patient}/${meta.id}/${it}" }, | ||
| enabled: true // just store normalised results | ||
| ], | ||
| [mode: params.publish_dir_mode, | ||
| path: { "${params.outdir}/reports/vt/${meta.variantcaller}/${meta.patient}/${meta.id}/" }, | ||
| pattern: "*stats" | ||
| ]] | ||
| } | ||
|
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| } | ||
| } |
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