diff --git a/hmftools.wdl b/hmftools.wdl
index 27badc9b8c90b37a83ad2d53fe81f1a579d061e1..b349038d55e8ce4fdf339030985aaaa1516faf8c 100644
--- a/hmftools.wdl
+++ b/hmftools.wdl
@@ -65,8 +65,8 @@ task Amber {
File tumorQc = "~{outputDir}/~{tumorName}.amber.qc"
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,
+ Array[File] outputs = [version, tumorBafPcf, tumorBafTsv, tumorBafVcf, tumorBafVcfIndex,
+ tumorContaminationVcf, tumorContaminationVcfIndex, tumorContaminationTsv, tumorQc,
normalSnpVcf, normalSnpVcfIndex]
}
@@ -110,7 +110,7 @@ task Cobalt {
File tumorBamIndex
String outputDir = "./cobalt"
File gcProfile
-
+
Int threads = 1
String memory = "5G"
String javaXmx = "4G"
@@ -174,7 +174,7 @@ task Cuppa {
Array[File]+ purpleOutput
String sampleName
Array[String]+ categories = ["DNA"]
- Array[File]+ referenceData
+ Array[File]+ referenceData
File purpleSvVcf
File purpleSvVcfIndex
File purpleSomaticVcf
@@ -244,7 +244,7 @@ task CuppaChart {
}
command {
- set -e
+ set -e
mkdir -p ~{outputDir}
cuppa-chart \
-sample ~{sampleName} \
@@ -429,7 +429,7 @@ task GripssHardFilterApplicationKt {
-cp /usr/local/share/hmftools-gripss-1.11-0/gripss.jar \
com.hartwig.hmftools.gripss.GripssHardFilterApplicationKt \
-input_vcf ~{inputVcf} \
- -output_vcf ~{outputPath}
+ -output_vcf ~{outputPath}
}
output {
@@ -490,7 +490,7 @@ task HealthChecker {
output {
Boolean succeeded = read_boolean("result")
- File outputFile = if succeeded
+ File outputFile = if succeeded
then "~{outputDir}/~{tumorName}.HealthCheckSucceeded"
else "~{outputDir}/~{tumorName}.HealthCheckFailed"
}
@@ -529,8 +529,6 @@ task Linx {
String outputDir = "./linx"
File fragileSiteCsv
File lineElementCsv
- File replicationOriginsBed
- File viralHostsCsv
File knownFusionCsv
File driverGenePanel
#The following should be in the same directory.
@@ -539,10 +537,10 @@ task Linx {
File transExonDataCsv
File transSpliceDataCsv
- String memory = "5G"
- String javaXmx = "4G"
+ String memory = "9G"
+ String javaXmx = "8G"
Int timeMinutes = 10
- String dockerImage = "quay.io/biocontainers/hmftools-linx:1.16--hdfd78af_0"
+ String dockerImage = "quay.io/biocontainers/hmftools-linx:1.17--hdfd78af_0"
}
command {
@@ -554,9 +552,7 @@ task Linx {
-output_dir ~{outputDir} \
-fragile_site_file ~{fragileSiteCsv} \
-line_element_file ~{lineElementCsv} \
- -replication_origins_file ~{replicationOriginsBed} \
- -viral_hosts_file ~{viralHostsCsv} \
- -gene_transcripts_dir ~{sub(geneDataCsv, basename(geneDataCsv), "")} \
+ -ensembl_data_dir ~{sub(geneDataCsv, basename(geneDataCsv), "")} \
-check_fusions \
-known_fusion_file ~{knownFusionCsv} \
-check_drivers \
@@ -598,12 +594,10 @@ task Linx {
svVcf: {description: "A VCF file containing structural variants, produced using GRIDSS, annotated for viral insertions and postprocessed with GRIPSS.", category: "required"}
svVcfIndex: {description: "Index for the structural variants VCf file.", category: "required"}
purpleOutput: {description: "The files produced by PURPLE.", category: "required"}
- refGenomeVersion: {description: "The version of the genome assembly used for alignment. Either \"HG19\" or \"HG38\".", category: "required"}
+ refGenomeVersion: {description: "The version of the genome assembly used for alignment. Either \"37\" or \"38\".", category: "required"}
outputDir: {description: "The directory the outputs will be written to.", category: "required"}
fragileSiteCsv: {description: "A list of known fragile sites.", category: "required"}
lineElementCsv: {description: "A list of known LINE source regions.", category: "required"}
- replicationOriginsBed: {description: "Replication timing input in BED format with replication timing as the 4th column.", category: "required"}
- viralHostsCsv: {description: "A list of the viruses which were used for annotation of the GRIDSS results.", category: "required"}
knownFusionCsv: {description: "A CSV file describing known fusions.", category: "required"}
driverGenePanel: {description: "A TSV file describing the driver gene panel.", category: "required"}
geneDataCsv: {description: "A CSV file containing gene information, must be in the same directory as `proteinFeaturesCsv`, `transExonDataCsv` and `transSpliceDataCsv`.", category: "required"}
@@ -675,10 +669,9 @@ task Pave {
referenceFasta: {description: "The reference fasta file.", category: "required"}
referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.",
category: "required"}
- referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
+ referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
refGenomeVersion: {description: "The version of the genome assembly used for alignment. Either \"HG19\" or \"HG38\".", category: "required"}
driverGenePanel: {description: "A TSV file describing the driver gene panel.", category: "required"}
- #The following should be in the same directory.
geneDataCsv: {description: "A CSV file containing gene information, must be in the same directory as `proteinFeaturesCsv`, `transExonDataCsv` and `transSpliceDataCsv`.", category: "required"}
proteinFeaturesCsv: {description: "A CSV file containing protein feature information, must be in the same directory as `geneDataCsv`, `transExonDataCsv` and `transSpliceDataCsv`.", category: "required"}
transExonDataCsv: {description: "A CSV file containing transcript exon information, must be in the same directory as `geneDataCsv`, `proteinFeaturesCsv` and `transSpliceDataCsv`.", category: "required"}
@@ -757,7 +750,7 @@ task Protect {
}
parameter_meta {
- refGenomeVersion: {description: "The version of the genome assembly used for alignment. Either \"37\" or \"38\".", category: "required"}
+ 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"}
referenceName: {description: "The name of the normal sample.", category: "required"}
sampleDoids: {description: "The DOIDs (Human Disease Ontology) for the primary tumor.", category: "required"}
@@ -800,41 +793,47 @@ task Purple {
File germlineVcf
File filteredSvVcf
File filteredSvVcfIndex
- File? fullSvVcf
- File? fullSvVcfIndex
+ File fullSvVcf
+ File fullSvVcfIndex
File referenceFasta
File referenceFastaFai
File referenceFastaDict
File driverGenePanel
File somaticHotspots
File germlineHotspots
-
+ #The following should be in the same directory.
+ File geneDataCsv
+ File proteinFeaturesCsv
+ File transExonDataCsv
+ File transSpliceDataCsv
+
Int threads = 1
Int timeMinutes = 30
String memory = "9G"
String javaXmx = "8G"
- # clone of quay.io/biocontainers/hmftools-purple:3.1--hdfd78af_0 with 'ln -s /usr/local/lib/libwebp.so.7 /usr/local/lib/libwebp.so.6'
- String dockerImage = "quay.io/biowdl/hmftools-purple:3.1"
+ # clone of quay.io/biocontainers/hmftools-purple:3.2--hdfd78af_0 with 'ln -s /usr/local/lib/libwebp.so.7 /usr/local/lib/libwebp.so.6'
+ String dockerImage = "quay.io/biowdl/hmftools-purple:3.2"
}
command {
PURPLE -Xmx~{javaXmx} \
-reference ~{referenceName} \
+ -germline_vcf ~{germlineVcf} \
+ -germline_hotspots ~{germlineHotspots} \
-tumor ~{tumorName} \
-output_dir ~{outputDir} \
-amber ~{sub(amberOutput[0], basename(amberOutput[0]), "")} \
-cobalt ~{sub(cobaltOutput[0], basename(cobaltOutput[0]), "")} \
-gc_profile ~{gcProfile} \
-somatic_vcf ~{somaticVcf} \
- -germline_vcf ~{germlineVcf} \
-structural_vcf ~{filteredSvVcf} \
- ~{"-sv_recovery_vcf " + fullSvVcf} \
+ -sv_recovery_vcf ~{fullSvVcf} \
-circos /usr/local/bin/circos \
-ref_genome ~{referenceFasta} \
- -driver_catalog \
- -driver_gene_panel ~{driverGenePanel} \
+ -ensembl_data_dir ~{sub(geneDataCsv, basename(geneDataCsv), "")} \
+ -run_drivers \
-somatic_hotspots ~{somaticHotspots} \
- -germline_hotspots ~{germlineHotspots} \
+ -driver_gene_panel ~{driverGenePanel} \
-threads ~{threads}
}
@@ -877,8 +876,8 @@ task Purple {
File circosMap = "~{outputDir}/circos/~{tumorName}.map.circos"
File circosSnp = "~{outputDir}/circos/~{tumorName}.snp.circos"
Array[File] outputs = [driverCatalogSomaticTsv, purpleCnvGeneTsv, purpleCnvGermlineTsv,
- purpleCnvSomaticTsv, purplePurityRangeTsv, purplePurityTsv, purpleQc,
- purpleSegmentTsv, purpleSomaticClonalityTsv, purpleSomaticHistTsv,
+ purpleCnvSomaticTsv, purplePurityRangeTsv, purplePurityTsv, purpleQc,
+ purpleSegmentTsv, purpleSomaticClonalityTsv, purpleSomaticHistTsv,
purpleSomaticVcf, purpleSomaticVcfIndex, purpleSvVcf, purpleSvVcfIndex,
purpleVersion, purpleGermlineVcf, purpleGermlineVcfIndex, driverCatalogGermlineTsv]
Array[File] plots = [circosPlot, copynumberPlot, inputPlot, mapPlot, purityRangePlot,
@@ -913,6 +912,11 @@ task Purple {
driverGenePanel: {description: "A TSV file describing the driver gene panel.", category: "required"}
somaticHotspots: {description: "A vcf file with hotspot somatic variant sites.", category: "required"}
germlineHotspots: {description: "A vcf file with hotspot germline variant sites.", category: "required"}
+ geneDataCsv: {description: "A CSV file containing gene information, must be in the same directory as `proteinFeaturesCsv`, `transExonDataCsv` and `transSpliceDataCsv`.", category: "required"}
+ proteinFeaturesCsv: {description: "A CSV file containing protein feature information, must be in the same directory as `geneDataCsv`, `transExonDataCsv` and `transSpliceDataCsv`.", category: "required"}
+ transExonDataCsv: {description: "A CSV file containing transcript exon information, must be in the same directory as `geneDataCsv`, `proteinFeaturesCsv` and `transSpliceDataCsv`.", category: "required"}
+ transSpliceDataCsv: {description: "A CSV file containing transcript splicing information, must be in the same directory as `geneDataCsv`, `proteinFeaturesCsv` and `transExonDataCsv`.", category: "required"}
+
threads: {description: "The number of threads the program will use.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
diff --git a/peach.wdl b/peach.wdl
index af44daecfc342630d78866d93767b260147d1a0e..6a5770f45771cd64155bcd53220ac74a6e561d29 100644
--- a/peach.wdl
+++ b/peach.wdl
@@ -22,7 +22,6 @@ version 1.0
task Peach {
input {
- File transcriptTsv
File germlineVcf
File germlineVcfIndex
String tumorName
@@ -31,28 +30,26 @@ task Peach {
File panelJson
String memory = "2G"
- String dockerImage = "quay.io/biowdl/peach:v1.0"
+ String dockerImage = "quay.io/biowdl/peach:v1.5"
Int timeMinutes = 5
}
command {
+ set -e
+ mkdir -p ~{outputDir}
peach \
- --recreate_bed \
- --transcript_tsv ~{transcriptTsv} \
- ~{germlineVcf} \
- ~{tumorName} \
- ~{normalName} \
- 1.0 \
- ~{outputDir} \
- ~{panelJson} \
- vcftools
+ -vcf ~{germlineVcf} \
+ --sample_t_id ~{tumorName} \
+ --sample_r_id ~{normalName} \
+ --tool_version 1.5 \
+ --outputDir ~{outputDir} \
+ --panel
}
output {
File callsTsv = "~{outputDir}/~{tumorName}.peach.calls.tsv"
- File filteredVcf = "~{outputDir}/~{tumorName}.peach.filtered.vcf"
File genotypeTsv = "~{outputDir}/~{tumorName}.peach.genotype.tsv"
- Array[File] outputs = [callsTsv, filteredVcf, genotypeTsv]
+ Array[File] outputs = [callsTsv, genotypeTsv]
}
runtime {
@@ -62,7 +59,6 @@ task Peach {
}
parameter_meta {
- transcriptTsv: {description: "A tsv file describing transcripts.", category: "required"}
germlineVcf: {description: "The germline VCF file from hmftools' purple.", category: "required"}
germlineVcfIndex: {description: "The germline VCF's index.", category: "required"}
tumorName: {description: "The name of the tumor sample.", category: "required"}
@@ -74,4 +70,4 @@ task Peach {
memory: {description: "The amount of memory available to the job.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
}
-}
\ No newline at end of file
+}