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version 1.0
import "common.wdl" as common
input {
String? preCommand
String? installDir
File? inclusionRegion
File? exclusionRegion
IndexedBamFile tumorBam
IndexedBamFile normalBam
File? mutect2VCF
File? varscanSNV
File? varscanIndel
File? jsmVCF
File? somaticsniperVCF
File? vardictVCF
File? museVCF
File? lofreqSNV
File? lofreqIndel
File? scalpelVCF
File? strelkaSNV
File? strelkaIndel
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Int threads = 1
}
String toolCommand = if defined(installDir)
then installDir + "/somaticseq_parallel.py"
else "/opt/somaticseq/somaticseq_parallel.py"
# else here points to the location in the docker image
command {
set -e -o pipefail
~{preCommand}
~{toolCommand} \
~{"--classifier-snv " + classifierSNV} \
~{"--classifier-indel " + classifierIndel} \
--output-directory ~{outputDir} \
--genome-reference ~{reference.fasta} \
~{"--inclusion-region " + inclusionRegion} \
~{"--exclusion-region " + exclusionRegion} \
--threads ~{threads} \
paired \
--tumor-bam-file ~{tumorBam.file} \
--normal-bam-file ~{normalBam.file} \
~{"--mutect2-vcf " + mutect2VCF} \
~{"--varscan-snv " + varscanSNV} \
~{"--varscan-indel " + varscanIndel} \
~{"--jsm-vcf " + jsmVCF} \
~{"--somaticsniper-vcf " + somaticsniperVCF} \
~{"--vardict-vcf " + vardictVCF} \
~{"--muse-vcf " + museVCF} \
~{"--lofreq-snv " + lofreqSNV} \
~{"--lofreq-indel " + lofreqIndel} \
~{"--scalpel-vcf " + scalpelVCF} \
~{"--strelka-snv " + strelkaSNV} \
~{"--strelka-indel " + strelkaIndel}
}
output {
File indels = outputDir + if defined(classifierIndel)
then "/SSeq.Classified.sINDEL.vcf"
else "/Consensus.sINDEL.vcf"
File snvs = outputDir + if defined(classifierSNV)
then "/SSeq.Classified.sSNV.vcf"
else "/Consensus.sSNV.vcf"
File ensembleIndels = outputDir + "/Ensemble.sINDEL.tsv"
File ensembleSNV = outputDir + "/Ensemble.sSNV.tsv"
}
runtime {
cpu: threads
docker: "lethalfang/somaticseq:3.1.0"
}
}
task SomaticSeqParallelPairedTrain {
input {
String? preCommand
String? installDir
File truthSNV
File truthIndel
String outputDir
Reference reference
File? inclusionRegion
File? exclusionRegion
IndexedBamFile tumorBam
IndexedBamFile normalBam
File? mutect2VCF
File? varscanSNV
File? varscanIndel
File? jsmVCF
File? somaticsniperVCF
File? vardictVCF
File? museVCF
File? lofreqSNV
File? lofreqIndel
File? scalpelVCF
File? strelkaSNV
File? strelkaIndel
Int threads = 1
}
String toolCommand = if defined(installDir)
then installDir + "/somaticseq_parallel.py"
else "/opt/somaticseq/somaticseq_parallel.py"
# else here points to the location in the docker image
command {
set -e -o pipefail
~{preCommand}
~{toolCommand} \
--somaticseq-train \
--truth-snv ~{truthSNV} \
--truth-indel ~{truthIndel} \
--output-directory ~{outputDir} \
~{"--exclusion-region " + exclusionRegion} \
--threads ~{threads} \
paired \
--tumor-bam-file ~{tumorBam.file} \
--normal-bam-file ~{normalBam.file} \
~{"--mutect2-vcf " + mutect2VCF} \
~{"--varscan-snv " + varscanSNV} \
~{"--varscan-indel " + varscanIndel} \
~{"--jsm-vcf " + jsmVCF} \
~{"--somaticsniper-vcf " + somaticsniperVCF} \
~{"--vardict-vcf " + vardictVCF} \
~{"--muse-vcf " + museVCF} \
~{"--lofreq-snv " + lofreqSNV} \
~{"--lofreq-indel " + lofreqIndel} \
~{"--strelka-snv " + strelkaSNV} \
~{"--strelka-indel " + strelkaIndel}
}
output {
File consensusIndels = outputDir + "/Consensus.sINDEL.vcf"
File consensusSNV = outputDir + "/Consensus.sSNV.vcf"
File ensembleIndels = outputDir + "/Ensemble.sINDEL.tsv"
File ensembleSNV = outputDir + "/Ensemble.sSNV.tsv"
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File ensembleIndelsClassifier = outputDir + "/Ensemble.sINDEL.tsv.ntChange.Classifier.RData"
File ensembleSNVClassifier = outputDir + "/Ensemble.sSNV.tsv.ntChange.Classifier.RData"
}
runtime {
cpu: threads
docker: "lethalfang/somaticseq:3.1.0"
}
}
task SomaticSeqParallelSingle {
input {
String? preCommand
String? installDir
File? classifierSNV
File? classifierIndel
String outputDir
Reference reference
File? inclusionRegion
File? exclusionRegion
IndexedBamFile bam
File? mutect2VCF
File? varscanVCF
File? vardictVCF
File? lofreqVCF
File? scalpelVCF
File? strelkaVCF
Int threads = 1
}
String toolCommand = if defined(installDir)
then installDir + "/somaticseq_parallel.py"
else "/opt/somaticseq/somaticseq_parallel.py"
# else here points to the location in the docker image
command {
set -e -o pipefail
~{preCommand}
~{toolCommand} \
~{"--classifier-snv " + classifierSNV} \
~{"--classifier-indel " + classifierIndel} \
--output-directory ~{outputDir} \
--genome-reference ~{reference.fasta} \
~{"--inclusion-region " + inclusionRegion} \
~{"--exclusion-region " + exclusionRegion} \
--threads ~{threads} \
single \
--bam-file ~{bam.file} \
~{"--mutect2-vcf " + mutect2VCF} \
~{"--varscan-vcf " + varscanVCF} \
~{"--vardict-vcf " + vardictVCF} \
~{"--lofreq-vcf " + lofreqVCF} \
~{"--scalpel-vcf " + scalpelVCF} \
~{"--strelka-vcf " + strelkaVCF}
}
output {
File indels = outputDir + if defined(classifierIndel)
then "/SSeq.Classified.sINDEL.vcf"
else "/Consensus.sINDEL.vcf"
File snvs = outputDir + if defined(classifierSNV)
then "/SSeq.Classified.sSNV.vcf"
else "/Consensus.sSNV.vcf"
File ensembleIndels = outputDir + "/Ensemble.sINDEL.tsv"
File ensembleSNV = outputDir + "/Ensemble.sSNV.tsv"
}
runtime {
cpu: threads
docker: "lethalfang/somaticseq:3.1.0"
input {
String? preCommand
String? installDir
File? inclusionRegion
File? exclusionRegion
File? mutect2VCF
File? varscanVCF
File? vardictVCF
File? lofreqVCF
File? scalpelVCF
File? strelkaVCF
}
String toolCommand = if defined(installDir)
then installDir + "/somaticseq_parallel.py"
else "/opt/somaticseq/somaticseq_parallel.py"
# else here points to the location in the docker image
command {
set -e -o pipefail
~{preCommand}
~{toolCommand} \
--somaticseq-train \
--truth-snv ~{truthSNV} \
--truth-indel ~{truthIndel} \
--output-directory ~{outputDir} \
~{"--exclusion-region " + exclusionRegion} \
--threads ~{threads} \
single \
--bam-file ~{bam.file} \
~{"--mutect2-vcf " + mutect2VCF} \
~{"--varscan-vcf " + varscanVCF} \
~{"--vardict-vcf " + vardictVCF} \
~{"--lofreq-vcf " + lofreqVCF} \
~{"--scalpel-vcf " + scalpelVCF} \
~{"--strelka-vcf " + strelkaVCF}
File consensusIndels = outputDir + "/Consensus.sINDEL.vcf"
File consensusSNV = outputDir + "/Consensus.sSNV.vcf"
File ensembleIndels = outputDir + "/Ensemble.sINDEL.tsv"
File ensembleSNV = outputDir + "/Ensemble.sSNV.tsv"
File ensembleIndelsClassifier = outputDir + "/Ensemble.sINDEL.tsv.ntChange.Classifier.RData"
File ensembleSNVClassifier = outputDir + "/Ensemble.sSNV.tsv.ntChange.Classifier.RData"