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Merge pull request nf-core#1193 from nf-core/sentieon_dnascope
Dnascope module and subworkflow in Sarek
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,68 @@ | ||
| /* | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| 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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| // SENTIEON DNASCOPE | ||
|
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| process { | ||
|
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| withName: 'SENTIEON_DNASCOPE' { | ||
| ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.dnascope" : "${meta.id}.dnascope.${intervals.simpleName}" } | ||
| ext.when = { params.tools && params.tools.split(',').contains('sentieon_dnascope') } | ||
| publishDir = [ | ||
| mode: params.publish_dir_mode, | ||
| path: { "${params.outdir}/variant_calling/"}, | ||
| pattern: "*{vcf.gz,vcf.gz.tbi}", | ||
| saveAs: { meta.num_intervals > 1 ? null : "sentieon_dnascope/${meta.id}/${it}" } | ||
| ] | ||
| } | ||
|
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| withName: 'MERGE_SENTIEON_DNASCOPE_VCFS' { | ||
| ext.prefix = { params.joint_germline ? "${meta.id}.dnascope.g" : "${meta.id}.dnascope.unfiltered" } | ||
| publishDir = [ | ||
| mode: params.publish_dir_mode, | ||
| path: { "${params.outdir}/variant_calling/sentieon_dnascope/${meta.id}/" }, | ||
| saveAs: { filename -> filename.equals('versions.yml') ? null : filename } | ||
| ] | ||
| } | ||
|
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| withName: 'MERGE_SENTIEON_DNASCOPE_GVCFS' { | ||
| ext.prefix = { "${meta.id}.dnascope.g" } | ||
| publishDir = [ | ||
| mode: params.publish_dir_mode, | ||
| path: { "${params.outdir}/variant_calling/sentieon_dnascope/${meta.id}/" }, | ||
| saveAs: { filename -> filename.equals('versions.yml') ? null : filename } | ||
| ] | ||
| } | ||
|
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| if (params.tools && params.tools.contains('sentieon_dnascope')) { | ||
| withName: '.*FILTERVARIANTTRANCHES' { | ||
| ext.prefix = {"${meta.id}.dnascope"} | ||
| ext.args = { "--info-key CNN_1D" } | ||
| publishDir = [ | ||
| mode: params.publish_dir_mode, | ||
| path: { "${params.outdir}/variant_calling/sentieon_dnascope/${meta.id}/"}, | ||
| pattern: "*{vcf.gz,vcf.gz.tbi}" | ||
| ] | ||
| } | ||
| } | ||
|
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| withName: 'SENTIEON_DNAMODELAPPLY' { | ||
| ext.prefix = {"${meta.id}.dnascope.filtered"} | ||
| publishDir = [ | ||
| mode: params.publish_dir_mode, | ||
| path: { "${params.outdir}/variant_calling/sentieon_dnascope/${meta.id}/"}, | ||
| pattern: "*{vcf.gz,vcf.gz.tbi}" | ||
| ] | ||
| } | ||
|
|
||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,45 @@ | ||
| /* | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| 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. | ||
| ---------------------------------------------------------------------------------------- | ||
| */ | ||
|
|
||
| // SENTIEON DNASCOPE JOINT_GERMLINE | ||
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| process { | ||
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| // TO-DO: duplicate!! | ||
| withName: 'SENTIEON_GVCFTYPER' { | ||
| ext.args = { "--allow-old-rms-mapping-quality-annotation-data" } | ||
| ext.prefix = { meta.intervals_name } | ||
| publishDir = [ | ||
| enabled: false | ||
| ] | ||
| } | ||
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| if (params.tools && params.tools.contains('sentieon_dnascope') && params.joint_germline) { | ||
| withName: 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_SENTIEON:BCFTOOLS_SORT' { | ||
| ext.prefix = { vcf.baseName - ".vcf" + ".sort" } | ||
| publishDir = [ | ||
| enabled: false | ||
| ] | ||
| } | ||
|
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| withName: 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_SENTIEON:MERGE_GENOTYPEGVCFS' { | ||
| ext.prefix = "joint_germline" | ||
| publishDir = [ | ||
| mode: params.publish_dir_mode, | ||
| path: { "${params.outdir}/variant_calling/sentieon_dnascope/joint_variant_calling/" }, | ||
| saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, | ||
| pattern: "*{vcf.gz,vcf.gz.tbi}" | ||
| ] | ||
| } | ||
| } | ||
| } |
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