Merge pull request #742 from MaxUlysse/HOTFIX

Fix output directories
SciLifeLab · Mar 4, 2019 · a4ed8f3 · a4ed8f3
2 parents 7f7f2c2 + 8ca0194
commit a4ed8f3
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,6 +5,11 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
+## [2.3.FIX1] - 2019-03-04
+
+### `Fixed`
+-   [#742](https://github.com/SciLifeLab/Sarek/pull/742) - Fix output dirs (HaplotypeCaller that was not recognized by annotate.nf introduced by [#728](https://github.com/SciLifeLab/Sarek/pull/728))
+
 ## [2.3] - Äpar - 2019-02-27
 
 ### `Added`

diff --git a/germlineVC.nf b/germlineVC.nf
@@ -249,21 +249,21 @@ process RunHaplotypecaller {
     ])
 
   output:
-    set val("gvcf-hc"), idPatient, idSample, idSample, file("${intervalBed.baseName}_${idSample}.g.vcf") into hcGenomicVCF
+    set val("HaplotypeCallerGVCF"), idPatient, idSample, idSample, file("${intervalBed.baseName}_${idSample}.g.vcf") into hcGenomicVCF
     set idPatient, idSample, file(intervalBed), file("${intervalBed.baseName}_${idSample}.g.vcf") into vcfsToGenotype
 
   when: 'haplotypecaller' in tools && !params.onlyQC
 
   script:
   """
   gatk --java-options "-Xmx${task.memory.toGiga()}g -Xms6000m -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10" \
-      HaplotypeCaller \
-      -R ${genomeFile} \
-      -I ${bam} \
-      -L ${intervalBed} \
-      --dbsnp ${dbsnp} \
-      -O ${intervalBed.baseName}_${idSample}.g.vcf \
-      --emit-ref-confidence GVCF
+    HaplotypeCaller \
+    -R ${genomeFile} \
+    -I ${bam} \
+    -L ${intervalBed} \
+    -D ${dbsnp} \
+    -O ${intervalBed.baseName}_${idSample}.g.vcf \
+    -ERC GVCF
   """
 }
 hcGenomicVCF = hcGenomicVCF.groupTuple(by:[0,1,2,3])
@@ -284,22 +284,23 @@ process RunGenotypeGVCFs {
     ])
 
   output:
-    set val("haplotypecaller"), idPatient, idSample, idSample, file("${intervalBed.baseName}_${idSample}.vcf") into hcGenotypedVCF
+    set val("HaplotypeCaller"), idPatient, idSample, idSample, file("${intervalBed.baseName}_${idSample}.vcf") into hcGenotypedVCF
 
   when: 'haplotypecaller' in tools && !params.onlyQC
 
   script:
   // Using -L is important for speed and we have to index the interval files also
   """
-  gatk IndexFeatureFile -F ${gvcf}
+  gatk --java-options -Xmx${task.memory.toGiga()}g \
+    IndexFeatureFile -F ${gvcf}
 
   gatk --java-options -Xmx${task.memory.toGiga()}g \
-  GenotypeGVCFs \
-  -R ${genomeFile} \
-  -L ${intervalBed} \
-  --dbsnp ${dbsnp} \
-  -V ${gvcf} \
-  -O ${intervalBed.baseName}_${idSample}.vcf
+    GenotypeGVCFs \
+    -R ${genomeFile} \
+    -L ${intervalBed} \
+    -D ${dbsnp} \
+    -V ${gvcf} \
+    -O ${intervalBed.baseName}_${idSample}.vcf
   """
 }
 hcGenotypedVCF = hcGenotypedVCF.groupTuple(by:[0,1,2,3])
@@ -331,8 +332,8 @@ process ConcatVCF {
   when: ( 'haplotypecaller' in tools || 'mutect2' in tools || 'freebayes' in tools ) && !params.onlyQC
 
   script:
-  if (variantCaller == 'haplotypecaller') outputFile = "${variantCaller}_${idSampleNormal}.vcf"
-  else if (variantCaller == 'gvcf-hc') outputFile = "haplotypecaller_${idSampleNormal}.g.vcf"
+  if (variantCaller == 'HaplotypeCaller') outputFile = "${variantCaller}_${idSampleNormal}.vcf"
+  else if (variantCaller == 'HaplotypeCallerGVCF') outputFile = "haplotypecaller_${idSampleNormal}.g.vcf"
   else outputFile = "${variantCaller}_${idSampleTumor}_vs_${idSampleNormal}.vcf"
   options = params.targetBED ? "-t ${targetBED}" : ""
   """
@@ -361,7 +362,7 @@ process RunSingleStrelka {
     ])
 
   output:
-    set val("singlestrelka"), idPatient, idSample,  file("*.vcf.gz"), file("*.vcf.gz.tbi") into singleStrelkaOutput
+    set val("Strelka"), idPatient, idSample,  file("*.vcf.gz"), file("*.vcf.gz.tbi") into singleStrelkaOutput
 
   when: 'strelka' in tools && !params.onlyQC
 
@@ -405,7 +406,7 @@ process RunSingleManta {
     ])
 
   output:
-    set val("singlemanta"), idPatient, idSample,  file("*.vcf.gz"), file("*.vcf.gz.tbi") into singleMantaOutput
+    set val("Manta"), idPatient, idSample,  file("*.vcf.gz"), file("*.vcf.gz.tbi") into singleMantaOutput
 
   when: 'manta' in tools && status == 0 && !params.onlyQC
 

diff --git a/somaticVC.nf b/somaticVC.nf
@@ -212,7 +212,7 @@ process RunMutect2 {
     ])
 
   output:
-    set val("mutect2"), idPatient, idSampleNormal, idSampleTumor, file("${intervalBed.baseName}_${idSampleTumor}_vs_${idSampleNormal}.vcf") into mutect2Output
+    set val("MuTect2"), idPatient, idSampleNormal, idSampleTumor, file("${intervalBed.baseName}_${idSampleTumor}_vs_${idSampleNormal}.vcf") into mutect2Output
 
   when: 'mutect2' in tools && !params.onlyQC
 
@@ -242,7 +242,7 @@ process RunFreeBayes {
     file(genomeIndex) from Channel.value(referenceMap.genomeIndex)
 
   output:
-    set val("freebayes"), idPatient, idSampleNormal, idSampleTumor, file("${intervalBed.baseName}_${idSampleTumor}_vs_${idSampleNormal}.vcf") into freebayesOutput
+    set val("FreeBayes"), idPatient, idSampleNormal, idSampleTumor, file("${intervalBed.baseName}_${idSampleTumor}_vs_${idSampleNormal}.vcf") into freebayesOutput
 
   when: 'freebayes' in tools && !params.onlyQC
 
@@ -322,7 +322,7 @@ process RunStrelka {
     ])
 
   output:
-    set val("strelka"), idPatient, idSampleNormal, idSampleTumor, file("*.vcf.gz"), file("*.vcf.gz.tbi") into strelkaOutput
+    set val("Strelka"), idPatient, idSampleNormal, idSampleTumor, file("*.vcf.gz"), file("*.vcf.gz.tbi") into strelkaOutput
 
   when: 'strelka' in tools && !params.onlyQC
 
@@ -367,7 +367,7 @@ process RunManta {
     ])
 
   output:
-    set val("manta"), idPatient, idSampleNormal, idSampleTumor, file("*.vcf.gz"), file("*.vcf.gz.tbi") into mantaOutput
+    set val("Manta"), idPatient, idSampleNormal, idSampleTumor, file("*.vcf.gz"), file("*.vcf.gz.tbi") into mantaOutput
     set idPatient, idSampleNormal, idSampleTumor, file("*.candidateSmallIndels.vcf.gz"), file("*.candidateSmallIndels.vcf.gz.tbi") into mantaToStrelka
 
   when: 'manta' in tools && !params.onlyQC
@@ -426,7 +426,7 @@ process RunSingleManta {
     ])
 
   output:
-    set val("singlemanta"), idPatient, idSample,  file("*.vcf.gz"), file("*.vcf.gz.tbi") into singleMantaOutput
+    set val("Manta"), idPatient, idSample,  file("*.vcf.gz"), file("*.vcf.gz.tbi") into singleMantaOutput
 
   when: 'manta' in tools && status == 1 && !params.onlyQC
 
@@ -491,7 +491,7 @@ process RunStrelkaBP {
     ])
 
   output:
-    set val("strelkaBP"), idPatient, idSampleNormal, idSampleTumor, file("*.vcf.gz"), file("*.vcf.gz.tbi") into strelkaBPOutput
+    set val("Strelka"), idPatient, idSampleNormal, idSampleTumor, file("*.vcf.gz"), file("*.vcf.gz.tbi") into strelkaBPOutput
 
   when: 'strelka' in tools && 'manta' in tools && params.strelkaBP && !params.onlyQC
 
@@ -605,7 +605,7 @@ process RunAscat {
     file(acLociGC) from Channel.value([referenceMap.acLociGC])
 
   output:
-    set val("ascat"), idPatient, idSampleNormal, idSampleTumor, file("${idSampleTumor}.*.{png,txt}") into ascatOutput
+    set val("ASCAT"), idPatient, idSampleNormal, idSampleTumor, file("${idSampleTumor}.*.{png,txt}") into ascatOutput
 
   when: 'ascat' in tools && !params.onlyQC