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version 1.0
import "common.wdl" as common
task SomaticSeqWrapper {
input {
String? preCommand
String? installDir
String outputDir
Reference ref
File? inclusionRegion
File? exclusionRegion
File tumorBam
File tumorIndex
File normalBam
File normalIndex
File? mutect2VCF
File? varscanSNV
File? varscanIndel
File? jsmVCF
File? somaticsniperVCF
File? vardictVCF
File? museVCF
File? lofreqSNV
File? lofreqIndel
File? scalpelVCF
File? strelkaSNV
File? strelkaIndel
}
String toolCommand = if defined(installDir)
then installDir + "/SomaticSeq.Wrapper.sh"
else "SomaticSeq.Wrapper.sh"
command {
set -e -o pipefail
~{preCommand}
~{toolCommand} \
--output-dir ~{outputDir} \
--genome-reference ~{ref.fasta} \
~{"--inclusion-region " + inclusionRegion} \
~{"--exclusion-region " + exclusionRegion} \
--tumor-bam ~{tumorBam} \
--normal-bam ~{normalBam} \
~{"--mutect2 " + mutect2VCF} \
~{"--varscan-snv " + varscanSNV} \
~{"--varscan-indel " + varscanIndel} \
~{"--jsm " + jsmVCF} \
~{"--sniper " + somaticsniperVCF} \
~{"--vardict " + vardictVCF} \
~{"--muse " + museVCF} \
~{"--lofreq-snv " + lofreqSNV} \
~{"--lofreq-indel " + lofreqIndel} \
~{"--scalpel " + scalpelVCF} \
~{"--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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}
}
task SsSomaticSeqWrapper {
input {
String? preCommand
String? installDir
String outputDir
Reference ref
File? inclusionRegion
File? exclusionRegion
File bam
File bamIndex
File? mutect2VCF
File? varscanVCF
File? vardictVCF
File? lofreqVCF
File? scalpelVCF
File? strelkaVCF
}
String toolCommand = if defined(installDir)
then installDir + "/ssSomaticSeq.Wrapper.sh"
else "ssSomaticSeq.Wrapper.sh"
command {
set -e -o pipefail
~{preCommand}
~{toolCommand} \
--output-dir ~{outputDir} \
--genome-reference ~{ref.fasta} \
~{"--inclusion-region " + inclusionRegion} \
~{"--exclusion-region " + exclusionRegion} \
--in-bam ~{bam} \
~{"--mutect2 " + mutect2VCF} \
~{"--varscan " + varscanVCF} \
~{"--vardict " + vardictVCF} \
~{"--lofreq " + lofreqVCF} \
~{"--scalpel " + scalpelVCF} \
~{"--strelka " + strelkaVCF}
}
output {
File consensusIndels = outputDir + "/Consensus.ssINDEL.vcf"
File consensusSNV = outputDir + "/Consensus.ssSNV.vcf"
File ensembleIndels = outputDir + "/Ensemble.ssINDEL.tsv"
File ensembleSNV = outputDir + "/Ensemble.ssSNV.tsv"
}