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Merge pull request #10 from ramprasadn/gcnvcaller
Add germlinecnvcaller
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,88 @@ | ||
| /* | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| 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. | ||
| ---------------------------------------------------------------------------------------- | ||
| */ | ||
|
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| process { | ||
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| withName: '.*GERMLINECNVCALLER_COHORT.*' { | ||
| publishDir = [ | ||
| enabled: false | ||
| ] | ||
| } | ||
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| withName: '.*GERMLINECNVCALLER_COHORT:SAMTOOLS_FAIDX' { | ||
| ext.when = { params.fai.equals(null) } | ||
| publishDir = [ | ||
| mode: params.publish_dir_mode, | ||
| path: { "${params.outdir}/germlinecnvcaller/references" }, | ||
| saveAs: { filename -> filename.equals('versions.yml') ? null : filename } | ||
| ] | ||
| } | ||
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| withName: '.*GERMLINECNVCALLER_COHORT:PICARD_CREATESEQUENCEDICTIONARY' { | ||
| ext.when = { params.dict.equals(null) } | ||
| publishDir = [ | ||
| mode: params.publish_dir_mode, | ||
| path: { "${params.outdir}/germlinecnvcaller/references" }, | ||
| saveAs: { filename -> filename.equals('versions.yml') ? null : filename } | ||
| ] | ||
| } | ||
|
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| withName: '.*GERMLINECNVCALLER_COHORT:GATK4_PREPROCESSINTERVALS' { | ||
| ext.args = { ["--imr OVERLAPPING_ONLY", | ||
| "--padding ${params.padding}", | ||
| "--bin-length ${params.bin_length}"].join(" ") | ||
| } | ||
| } | ||
|
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| withName: '.*GERMLINECNVCALLER_COHORT:GATK4_COLLECTREADCOUNTS' { | ||
| ext.args = {"--format ${params.readcount_format} --imr OVERLAPPING_ONLY"} | ||
| publishDir = [ | ||
| mode: params.publish_dir_mode, | ||
| path: { "${params.outdir}/germlinecnvcaller/readcounts" }, | ||
| saveAs: { filename -> filename.equals('versions.yml') ? null : filename } | ||
| ] | ||
| } | ||
|
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| withName: '.*GERMLINECNVCALLER_COHORT:GATK4_ANNOTATEINTERVALS' { | ||
| ext.args = {"--imr OVERLAPPING_ONLY"} | ||
| ext.prefix = {" ${meta.id}_annotated"} | ||
| } | ||
|
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| withName: '.*GERMLINECNVCALLER_COHORT:GATK4_FILTERINTERVALS' { | ||
| ext.args = {"--imr OVERLAPPING_ONLY"} | ||
| ext.prefix = {" ${meta.id}_filtered"} | ||
| } | ||
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| withName: '.*GERMLINECNVCALLER_COHORT:GATK4_INTERVALLISTTOOLS' { | ||
| ext.args = {"--SUBDIVISION_MODE INTERVAL_COUNT --SCATTER_CONTENT ${params.scatter_content}"} | ||
| } | ||
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| withName: '.*GERMLINECNVCALLER_COHORT:GATK4_DETERMINEGERMLINECONTIGPLOIDY' { | ||
| ext.args = {"--imr OVERLAPPING_ONLY"} | ||
| publishDir = [ | ||
| mode: params.publish_dir_mode, | ||
| path: { "${params.outdir}/germlinecnvcaller/determinegermlinecontigploidy" }, | ||
| pattern: "*-model", | ||
| saveAs: { filename -> filename.equals('versions.yml') ? null : filename } | ||
| ] | ||
| } | ||
|
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| withName: '.*GERMLINECNVCALLER_COHORT:GATK4_GERMLINECNVCALLER' { | ||
| ext.args = {"--imr OVERLAPPING_ONLY --run-mode COHORT"} | ||
| publishDir = [ | ||
| mode: params.publish_dir_mode, | ||
| path: { "${params.outdir}/germlinecnvcaller/germlinecnvcaller" }, | ||
| saveAs: { filename -> filename.equals('versions.yml') ? null : filename } | ||
| ] | ||
| } | ||
|
|
||
| } |
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