diff --git a/hmftools.wdl b/hmftools.wdl
index 1537bce5c242fd879556d3bfaddc560ef116af64..0b4ba6d0ede70b4fecbac475fcded6fa5285f001 100644
--- a/hmftools.wdl
+++ b/hmftools.wdl
@@ -22,9 +22,9 @@ version 1.0
task Amber {
input {
- String normalName
- File normalBam
- File normalBamIndex
+ String referenceName
+ File referenceBam
+ File referenceBamIndex
String tumorName
File tumorBam
File tumorBamIndex
@@ -43,8 +43,8 @@ task Amber {
command {
AMBER -Xmx~{javaXmx} \
- -reference ~{normalName} \
- -reference_bam ~{normalBam} \
+ -reference ~{referenceName} \
+ -reference_bam ~{referenceBam} \
-tumor ~{tumorName} \
-tumor_bam ~{tumorBam} \
-output_dir ~{outputDir} \
@@ -63,8 +63,8 @@ task Amber {
File tumorContaminationVcfIndex = "~{outputDir}/~{tumorName}.amber.contamination.vcf.gz.tbi"
File tumorContaminationTsv = "~{outputDir}/~{tumorName}.amber.contamination.tsv"
File tumorQc = "~{outputDir}/~{tumorName}.amber.qc"
- File normalSnpVcf = "~{outputDir}/~{normalName}.amber.snp.vcf.gz"
- File normalSnpVcfIndex = "~{outputDir}/~{normalName}.amber.snp.vcf.gz.tbi"
+ File normalSnpVcf = "~{outputDir}/~{referenceName}.amber.snp.vcf.gz"
+ File normalSnpVcfIndex = "~{outputDir}/~{referenceName}.amber.snp.vcf.gz.tbi"
Array[File] outputs = [version, tumorBafPcf, tumorBafTsv, tumorBafVcf, tumorBafVcfIndex,
tumorContaminationVcf, tumorContaminationVcfIndex, tumorContaminationTsv, tumorQc,
normalSnpVcf, normalSnpVcfIndex]
@@ -78,9 +78,9 @@ task Amber {
}
parameter_meta {
- normalName: {description: "the name of the normal sample.", category: "required"}
- normalBam: {description: "The normal BAM file.", category: "required"}
- normalBamIndex: {description: "The index for the normal BAM file.", category: "required"}
+ referenceName: {description: "the name of the normal sample.", category: "required"}
+ referenceBam: {description: "The normal BAM file.", category: "required"}
+ referenceBamIndex: {description: "The index for the normal BAM file.", category: "required"}
tumorName: {description: "The name of the tumor sample.", category: "required"}
tumorBam: {description: "The tumor BAM file.", category: "required"}
tumorBamIndex: {description: "The index for the tumor BAM file.", category: "required"}
@@ -102,9 +102,9 @@ task Amber {
task Cobalt {
input {
- String normalName
- File normalBam
- File normalBamIndex
+ String referenceName
+ File referenceBam
+ File referenceBamIndex
String tumorName
File tumorBam
File tumorBamIndex
@@ -120,8 +120,8 @@ task Cobalt {
command {
COBALT -Xmx~{javaXmx} \
- -reference ~{normalName} \
- -reference_bam ~{normalBam} \
+ -reference ~{referenceName} \
+ -reference_bam ~{referenceBam} \
-tumor ~{tumorName} \
-tumor_bam ~{tumorBam} \
-output_dir ~{outputDir} \
@@ -131,9 +131,9 @@ task Cobalt {
output {
File version = "~{outputDir}/cobalt.version"
- File normalGcMedianTsv = "~{outputDir}/~{normalName}.cobalt.gc.median.tsv"
- File normalRationMedianTsv = "~{outputDir}/~{normalName}.cobalt.ratio.median.tsv"
- File normalRationPcf = "~{outputDir}/~{normalName}.cobalt.ratio.pcf"
+ File normalGcMedianTsv = "~{outputDir}/~{referenceName}.cobalt.gc.median.tsv"
+ File normalRationMedianTsv = "~{outputDir}/~{referenceName}.cobalt.ratio.median.tsv"
+ File normalRationPcf = "~{outputDir}/~{referenceName}.cobalt.ratio.pcf"
File tumorGcMedianTsv = "~{outputDir}/~{tumorName}.cobalt.gc.median.tsv"
File tumorRatioPcf = "~{outputDir}/~{tumorName}.cobalt.ratio.pcf"
File tumorRatioTsv = "~{outputDir}/~{tumorName}.cobalt.ratio.tsv"
@@ -150,9 +150,9 @@ task Cobalt {
}
parameter_meta {
- normalName: {description: "the name of the normal sample.", category: "required"}
- normalBam: {description: "The normal BAM file.", category: "required"}
- normalBamIndex: {description: "The index for the normal BAM file.", category: "required"}
+ referenceName: {description: "the name of the normal sample.", category: "required"}
+ referenceBam: {description: "The normal BAM file.", category: "required"}
+ referenceBamIndex: {description: "The index for the normal BAM file.", category: "required"}
tumorName: {description: "The name of the tumor sample.", category: "required"}
tumorBam: {description: "The tumor BAM file.", category: "required"}
tumorBamIndex: {description: "The index for the tumor BAM file.", category: "required"}
@@ -279,7 +279,7 @@ task GripssApplicationKt {
File inputVcf
String outputPath = "gripss.vcf.gz"
String tumorName
- String normalName
+ String referenceName
File referenceFasta
File referenceFastaFai
File referenceFastaDict
@@ -287,8 +287,8 @@ task GripssApplicationKt {
File breakendPon
File breakpointPon
- String memory = "33G"
- String javaXmx = "32G"
+ String memory = "32G"
+ String javaXmx = "31G"
Int timeMinutes = 45
String dockerImage = "quay.io/biocontainers/hmftools-gripss:1.11--hdfd78af_0"
}
@@ -298,7 +298,7 @@ task GripssApplicationKt {
-cp /usr/local/share/hmftools-gripss-1.11-0/gripss.jar \
com.hartwig.hmftools.gripss.GripssApplicationKt \
-tumor ~{tumorName} \
- -reference ~{normalName} \
+ -reference ~{referenceName} \
-ref_genome ~{referenceFasta} \
-breakpoint_hotspot ~{breakpointHotspot} \
-breakend_pon ~{breakendPon} \
@@ -383,9 +383,9 @@ task GripssHardFilterApplicationKt {
task HealthChecker {
input {
String outputDir = "."
- String normalName
- File normalFlagstats
- File normalMetrics
+ String referenceName
+ File referenceFlagstats
+ File referenceMetrics
String tumorName
File tumorFlagstats
File tumorMetrics
@@ -401,9 +401,9 @@ task HealthChecker {
set -e
mkdir -p ~{outputDir}
health-checker -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
- -reference ~{normalName} \
- -ref_flagstat_file ~{normalFlagstats} \
- -ref_wgs_metrics_file ~{normalMetrics} \
+ -reference ~{referenceName} \
+ -ref_flagstat_file ~{referenceFlagstats} \
+ -ref_wgs_metrics_file ~{referenceMetrics} \
-tumor ~{tumorName} \
-tum_flagstat_file ~{tumorFlagstats} \
-tum_wgs_metrics_file ~{tumorMetrics} \
@@ -425,9 +425,9 @@ task HealthChecker {
parameter_meta {
outputDir: {description: "The path the output will be written to.", category:"required"}
- normalName: {description: "The name of the normal sample.", category: "required"}
- normalFlagstats: {description: "The flagstats for the normal sample.", category: "required"}
- normalMetrics: {description: "The picard WGS metrics for the normal sample.", category: "required"}
+ referenceName: {description: "The name of the normal sample.", category: "required"}
+ referenceFlagstats: {description: "The flagstats for the normal sample.", category: "required"}
+ referenceMetrics: {description: "The picard WGS metrics for the normal sample.", category: "required"}
tumorName: {description: "The name of the tumor sample.", category: "required"}
tumorFlagstats: {description: "The flagstats for the tumor sample.", category: "required"}
tumorMetrics: {description: "The picard WGS metrics for the tumor sample.", category: "required"}
@@ -546,11 +546,11 @@ task Protect {
input {
String refGenomeVersion
String tumorName
- String normalName
+ String referenceName
Array[String]+ sampleDoids
String outputDir = "."
Array[File]+ serveActionability
- File doidsJson
+ File doidJson
File purplePurity
File purpleQc
File purpleDriverCatalogSomatic
@@ -576,11 +576,11 @@ task Protect {
protect -Xmx~{javaXmx} \
-ref_genome_version ~{refGenomeVersion} \
-tumor_sample_id ~{tumorName} \
- -reference_sample_id ~{normalName} \
+ -reference_sample_id ~{referenceName} \
-primary_tumor_doids '~{sep=";" sampleDoids}' \
-output_dir ~{outputDir} \
-serve_actionability_dir ~{sub(serveActionability[0], basename(serveActionability[0]), "")} \
- -doid_json ~{doidsJson} \
+ -doid_json ~{doidJson} \
-purple_purity_tsv ~{purplePurity} \
-purple_qc_file ~{purpleQc} \
-purple_somatic_driver_catalog_tsv ~{purpleDriverCatalogSomatic} \
@@ -608,11 +608,11 @@ task Protect {
parameter_meta {
refGenomeVersion: {description: "The version of the genome assembly used for alignment. Either \"37\" or \"38\".", category: "required"}
tumorName: {description: "The name of the tumor sample.", category: "required"}
- normalName: {description: "The name of the normal sample.", category: "required"}
+ referenceName: {description: "The name of the normal sample.", category: "required"}
sampleDoids: {description: "The DOIDs (Human Disease Ontology) for the primary tumor.", category: "required"}
outputDir: {description: "The directory the outputs will be written to.", category: "required"}
serveActionability: {description: "The actionability files generated by hmftools' serve.", category: "required"}
- doidsJson: {description: "A json with the DOID (Human Disease Ontology) tree.", category: "required"}
+ doidJson: {description: "A json with the DOID (Human Disease Ontology) tree.", category: "required"}
purplePurity: {description: "The purity file generated by purple.", category: "required"}
purpleQc: {description: "The QC file generated by purple.", category: "required"}
purpleDriverCatalogSomatic: {description: "The somatic driver catalog generated by purple.", category: "required"}
@@ -639,7 +639,7 @@ task Protect {
task Purple {
input {
- String normalName
+ String referenceName
String tumorName
String outputDir = "./purple"
Array[File]+ amberOutput
@@ -667,7 +667,7 @@ task Purple {
command {
PURPLE -Xmx~{javaXmx} \
- -reference ~{normalName} \
+ -reference ~{referenceName} \
-tumor ~{tumorName} \
-output_dir ~{outputDir} \
-amber ~{sub(amberOutput[0], basename(amberOutput[0]), "")} \
@@ -713,7 +713,7 @@ task Purple {
File somaticClonalityPlot = "~{outputDir}/plot/~{tumorName}.somatic.clonality.png"
File somaticPlot = "~{outputDir}/plot/~{tumorName}.somatic.png"
File purpleVersion = "~{outputDir}/purple.version"
- File circosNormalRatio = "~{outputDir}/circos/~{normalName}.ratio.circos"
+ File circosNormalRatio = "~{outputDir}/circos/~{referenceName}.ratio.circos"
File circosConf = "~{outputDir}/circos/~{tumorName}.circos.conf"
File circosIndel = "~{outputDir}/circos/~{tumorName}.indel.circos"
File circosLink = "~{outputDir}/circos/~{tumorName}.link.circos"
@@ -744,7 +744,7 @@ task Purple {
}
parameter_meta {
- normalName: {description: "the name of the normal sample.", category: "required"}
+ referenceName: {description: "the name of the normal sample.", category: "required"}
tumorName: {description: "The name of the tumor sample.", category: "required"}
outputDir: {description: "The path to the output directory.", category: "common"}
amberOutput: {description: "The output files of hmftools amber.", category: "required"}
@@ -787,9 +787,9 @@ task Sage {
Boolean panelOnly = false
String outputPath = "./sage.vcf.gz"
- String? normalName
- File? normalBam
- File? normalBamIndex
+ String? referenceName
+ File? referenceBam
+ File? referenceBamIndex
Int? hotspotMinTumorQual
Int? panelMinTumorQual
Int? hotspotMaxGermlineVaf
@@ -801,8 +801,8 @@ task Sage {
Int threads = 4
String javaXmx = "50G"
- String memory = "60G"
- Int timeMinutes = 1 + ceil(size(select_all([tumorBam, normalBam]), "G") * 9 / threads)
+ String memory = "51G"
+ Int timeMinutes = 1 + ceil(size(select_all([tumorBam, referenceBam]), "G") * 9 / threads)
String dockerImage = "quay.io/biocontainers/hmftools-sage:2.8--hdfd78af_0"
}
@@ -810,8 +810,8 @@ task Sage {
SAGE -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
-tumor ~{tumorName} \
-tumor_bam ~{tumorBam} \
- ~{"-reference " + normalName} \
- ~{"-reference_bam " + normalBam} \
+ ~{"-reference " + referenceName} \
+ ~{"-reference_bam " + referenceBam} \
-ref_genome ~{referenceFasta} \
-hotspots ~{hotspots} \
-panel_bed ~{panelBed} \
@@ -848,9 +848,9 @@ task Sage {
tumorName: {description: "The name of the tumor sample.", category: "required"}
tumorBam: {description: "The BAM file for the tumor sample.", category: "required"}
tumorBamIndex: {description: "The index of the BAM file for the tumor sample.", category: "required"}
- normalName: {description: "The name of the normal/reference sample.", category: "common"}
- normalBam: {description: "The BAM file for the normal sample.", category: "common"}
- normalBamIndex: {description: "The index of the BAM file for the normal sample.", category: "common"}
+ referenceName: {description: "The name of the normal/reference sample.", category: "common"}
+ referenceBam: {description: "The BAM file for the normal sample.", category: "common"}
+ referenceBamIndex: {description: "The index of the BAM file for the normal sample.", category: "common"}
referenceFasta: {description: "The reference fasta file.", category: "required"}
referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.",
category: "required"}