From bcb51b0a7f086d24aaa1abf90b5b5c331f144390 Mon Sep 17 00:00:00 2001
From: Anne Marie Noronha <anoronh4@users.noreply.github.com>
Date: Fri, 30 Jun 2023 13:26:34 -0400
Subject: [PATCH] Switched facets annotation to using hisens results rather
 than purity

---
 modules/process/Facets/DoFacets.nf                  | 2 +-
 modules/process/GermSNV/GermlineFacetsAnnotation.nf | 4 ++--
 modules/process/SNV/SomaticFacetsAnnotation.nf      | 4 ++--
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/modules/process/Facets/DoFacets.nf b/modules/process/Facets/DoFacets.nf
index 2fb940a0..76da00a7 100644
--- a/modules/process/Facets/DoFacets.nf
+++ b/modules/process/Facets/DoFacets.nf
@@ -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
diff --git a/modules/process/GermSNV/GermlineFacetsAnnotation.nf b/modules/process/GermSNV/GermlineFacetsAnnotation.nf
index 8bc5fb1b..c598529f 100644
--- a/modules/process/GermSNV/GermlineFacetsAnnotation.nf
+++ b/modules/process/GermSNV/GermlineFacetsAnnotation.nf
@@ -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
@@ -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
 
diff --git a/modules/process/SNV/SomaticFacetsAnnotation.nf b/modules/process/SNV/SomaticFacetsAnnotation.nf
index c51bb0b1..a8666f59 100644
--- a/modules/process/SNV/SomaticFacetsAnnotation.nf
+++ b/modules/process/SNV/SomaticFacetsAnnotation.nf
@@ -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
@@ -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