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Commit cfff4640 authored by Cats's avatar Cats
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Merge remote-tracking branch 'origin/sage' into sage

parents 0f6d75c7 54337a3c
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hmftools.wdl
+ 37
− 33
View file @ cfff4640
......@@ -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"}
......
peach.wdl
+ 11
− 15
View file @ cfff4640
......@@ -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
}
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