add somaticseq and add precommands to strelka/manta run

manta.wdl

@@ -2,6 +2,7 @@ version 1.0
 
 task ConfigureSomatic {
     input {
+        String? preCommand
         File tumorBam
         File tumorIndex
         File? normalBam
@@ -39,6 +40,7 @@ task ConfigureSomatic {
 
 task RunSomatic {
     input {
+        String? preCommand
         String runDir
         Int cores = 1
         Int memory = 4
@@ -46,6 +48,8 @@ task RunSomatic {
     }
 
     command {
+        set -e -o pipefail
+        ~{preCommand}
         ~{runDir}/runWorkflow.py \
         -m local \
         -j ~{cores} \

somaticseq.wdl

+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.vcf"
+        File ensembleSNV = outputDir + "/Ensemble.sSNV.vcf"
+    }
+}
+
+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}
+    }
+}
\ No newline at end of file

strelka.wdl

@@ -78,6 +78,7 @@ task ConfigureSomatic {
 
 task Run {
     input {
+        String? preCommand
         String runDir
         Int cores = 1
         Int memory = 4
@@ -85,6 +86,8 @@ task Run {
     }
 
     command {
+        set -e -o pipefail
+        ~{preCommand}
         ~{runDir}/runWorkflow.py \
         -m local \
         -j ~{cores} \