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Merge pull request #22 from LouisLeNezet/validation
Add validation step
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,33 @@ | ||
| /* | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| 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. | ||
| ---------------------------------------------------------------------------------------- | ||
| */ | ||
|
|
||
| process { | ||
| withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CONCAT_IMPUT:.*' { | ||
| publishDir = [ | ||
| path: { "${params.outdir}/imputation/concat" }, | ||
| mode: params.publish_dir_mode, | ||
| saveAs: { filename -> filename.equals('versions.yml') ? null : filename } | ||
| ] | ||
| ext.prefix = { "${meta.id}_impute_concat" } | ||
| } | ||
|
|
||
| withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CONCAT_IMPUT:BCFTOOLS_CONCAT' { | ||
| ext.args = {[ | ||
| "--ligate", | ||
| "--output-type z", | ||
| ].join(" ").trim()} | ||
| } | ||
|
|
||
| withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CONCAT_IMPUT:BCFTOOLS_INDEX' { | ||
| ext.args = "--tbi" | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,84 @@ | ||
| /* | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| 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. | ||
| ---------------------------------------------------------------------------------------- | ||
| */ | ||
|
|
||
| process { | ||
| // Configuration for the glimpse1 imputation subworkflow | ||
| withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:GL_INPUT:.*' { | ||
| publishDir = [ | ||
| path: { "${params.outdir}/imputation/glimpse1/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }, | ||
| mode: params.publish_dir_mode, | ||
| saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, | ||
| enabled: false | ||
| ] | ||
| } | ||
| withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:GL_INPUT:BCFTOOLS_MPILEUP' { | ||
| ext.args = [ | ||
| "-I", | ||
| "-E", | ||
| "-a 'FORMAT/DP'" | ||
| ].join(' ') | ||
| ext.args2 = [ | ||
| "-Aim", | ||
| "-C alleles" | ||
| ].join(' ') | ||
| ext.prefix = { "${meta.id}_R${meta.region.replace(':','_')}.call" } | ||
| } | ||
|
|
||
| withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:GL_INPUT:BCFTOOLS_ANNOTATE' { | ||
| ext.args = "--set-id '%CHROM:%POS:%REF:%ALT' -Oz" | ||
| ext.prefix = { "${meta.id}_R${meta.region.replace(':','_')}.annotate" } | ||
| } | ||
|
|
||
| withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:GL_INPUT:BCFTOOLS_INDEX' { | ||
| ext.args = "--tbi" | ||
| } | ||
|
|
||
| withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_IMPUTE_GLIMPSE1:.*' { | ||
| publishDir = [ | ||
| path: { "${params.outdir}/imputation/glimpse1/" }, | ||
| mode: params.publish_dir_mode, | ||
| saveAs: { filename -> filename.equals('versions.yml') ? null : filename } | ||
| ] | ||
| } | ||
|
|
||
| withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_IMPUTE_GLIMPSE1:GLIMPSE_CHUNK' { | ||
| ext.args = [ | ||
| "--window-size 200000", | ||
| "--buffer-size 20000" | ||
| ].join(' ') | ||
| ext.prefix = { "${meta.id}_R${meta.region.replace(':','_')}.chunk" } | ||
| publishDir = [ enabled: false ] | ||
| } | ||
|
|
||
| withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_IMPUTE_GLIMPSE1:GLIMPSE_PHASE' { | ||
| ext.args = [ | ||
| "--impute-reference-only-variants" | ||
| ].join(' ') | ||
| ext.prefix = { "${meta.id}_R${meta.region.replace(':','_')}.phase" } | ||
| ext.suffix = "bcf" | ||
| publishDir = [ enabled: false ] | ||
| } | ||
|
|
||
| withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_IMPUTE_GLIMPSE1:INDEX_PHASE' { | ||
| publishDir = [ enabled: false ] | ||
| } | ||
|
|
||
| withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_IMPUTE_GLIMPSE1:GLIMPSE_LIGATE' { | ||
| ext.prefix = { "${meta.id}_R${meta.region.replace(':','_')}.ligate" } | ||
| } | ||
|
|
||
| withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_IMPUTE_GLIMPSE1:INDEX_LIGATE' { | ||
| publishDir = [ | ||
| path: { "${params.outdir}/imputation/glimpse1" } | ||
| ] | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,21 @@ | ||
| /* | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| 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. | ||
| ---------------------------------------------------------------------------------------- | ||
| */ | ||
|
|
||
| process { | ||
| withName: 'PIPELINE_INITIALISATION:.*' { | ||
| publishDir = [ | ||
| path: { "${params.outdir}/initialisation/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }, | ||
| mode: params.publish_dir_mode, | ||
| enabled: false | ||
| ] | ||
| } | ||
| } |
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