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Fixed facets zygosity annotation of maf #987

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merged 1 commit into from
Dec 21, 2023
Merged

Fixed facets zygosity annotation of maf #987

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2 changes: 1 addition & 1 deletion modules/process/Facets/DoFacets.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@ process DoFacets {
path("${outputDir}/*"), emit: FacetsOutput
tuple val("placeHolder"), val(idTumor), val(idNormal), path("*/*_purity.seg"), path("*/*_hisens.seg"), path("*_OUT.txt"), path("*/*.arm_level.txt"), path("*/*.gene_level.txt"), emit: facets4Aggregate
tuple val(idTumor), val(idNormal), val(target), path("${outputDir}/*purity.out"), emit: facetsPurity
tuple val(idTumor), val(idNormal), val(target), path("${outputDir}/*purity.Rdata"), path("${outputDir}/*purity.cncf.txt"), path("${outputDir}/*hisens.cncf.txt"), val("${outputDir}"), emit: facetsForMafAnno
tuple val(idTumor), val(idNormal), val(target), path("${outputDir}/*hisens.Rdata"), val("${outputDir}"), emit: facetsForMafAnno
tuple val(idTumor), val(idNormal), val(target), path("${outputDir}/*.{Rdata,png,out,seg,txt}"), path("${idTumor}__${idNormal}.snp_pileup.gz"), val("${outputDir}"), emit: Facets4FacetsPreview
tuple val("placeHolder"), val(idTumor), val(idNormal), path("*/*.*_level.txt"), emit: FacetsArmGeneOutput
tuple val(idTumor), val(idNormal), val(target), path("*/*.qc.txt"), emit: FacetsQC4MetaDataParser
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4 changes: 2 additions & 2 deletions modules/process/GermSNV/GermlineFacetsAnnotation.nf
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Expand Up @@ -4,7 +4,7 @@ process GermlineFacetsAnnotation {
publishDir "${params.outDir}/germline/${idNormal}/combined_mutations/", mode: params.publishDirMode, pattern: "*.germline.final.maf"

input:
tuple val(idTumor), val(idNormal), val(target), path(purity_rdata), path(purity_cncf), path(hisens_cncf), val(facetsPath), path(maf)
tuple val(idTumor), val(idNormal), val(target), path(hisens_rdata), val(facetsPath), path(maf)

output:
path("${outputPrefix}.final.maf"), emit: mafFileOutputGermline
Expand All @@ -15,7 +15,7 @@ process GermlineFacetsAnnotation {
"""
if [ \$( cat ${maf} | wc -l ) -gt 1 ] ; then
Rscript --no-init-file /usr/bin/facets-suite/annotate-maf-wrapper.R \
--facets-output ${purity_rdata} \
--facets-output ${hisens_rdata} \
--maf-file ${maf} \
--output ${outputPrefix}.facets.maf

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4 changes: 2 additions & 2 deletions modules/process/SNV/SomaticFacetsAnnotation.nf
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Expand Up @@ -4,7 +4,7 @@ process SomaticFacetsAnnotation {
publishDir "${params.outDir}/somatic/${outputPrefix}/combined_mutations/", mode: params.publishDirMode, pattern: "*.somatic.final.maf"

input:
tuple val(idTumor), val(idNormal), val(target), path(purity_rdata), path(purity_cncf), path(hisens_cncf), val(facetsPath), path(maf)
tuple val(idTumor), val(idNormal), val(target), path(hisens_rdata), val(facetsPath), path(maf)

output:
tuple val("placeHolder"), val(idTumor), val(idNormal), path("${outputPrefix}.somatic.final.maf"), emit: finalMaf4Aggregate
Expand All @@ -17,7 +17,7 @@ process SomaticFacetsAnnotation {
"""
if [ \$( cat ${maf} | wc -l ) -gt 1 ] ; then
Rscript --no-init-file /usr/bin/facets-suite/annotate-maf-wrapper.R \
--facets-output ${purity_rdata} \
--facets-output ${hisens_rdata} \
--maf-file ${maf} \
--facets-algorithm em \
--output ${outputPrefix}.facets.maf
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