add manta

manta.wdl

+version 1.0
+
+task Somatic {
+    input {
+        File tumorBam
+        File tumorIndex
+        File? normalBam
+        File? normalIndex
+        File refFasta
+        String runDir
+        File? callRegions
+        File? callRegionsIndex
+        Boolean exome = false
+        String? preCommand
+        String? installDir
+
+        Int cores = 1
+        Int memory = 4
+    }
+
+    String toolCommand = if defined(installDir)
+        then installDir + "bin/configMata.py"
+        else "configManta.py"
+
+    command {
+        set -e -o pipefail
+        ~{preCommand}
+        ~{toolCommand} \
+        ~{"--normalBam " + normalBam} \
+        ~{"--tumorBam " + tumorBam} \
+        --referenceFasta ~{refFasta} \
+        ~{"--callRegions " + callRegions} \
+        --runDir ~{runDir} \
+        ~{true="--exome" false="" exome}
+
+        ~{installDir}/runWorkflow.py \
+        -m local \
+        -j ~{cores} \
+        -g ~{memory}
+    }
+
+    output {
+        File condidateSmallIndels = runDir + "/results/variants/candidateSmallIndels.vcf.gz"
+        File condidateSmallIndelsIndex = runDir +
+            "/results/variants/candidateSmallIndels.vcf.gz.tbi"
+        File candidateSV = runDir + "/results/variants/candidateSV.vcf.gz"
+        File candidateSVindex = runDir + "/results/variants/candidateSV.vcf.gz.tbi"
+        File tumorSV = if defined(normalBam)
+            then runDir + "/results/variants/somaticSV.vcf.gz"
+            else runDir + "/results/variants/tumorSV.vcf.gz"
+        File tumorSVindex = if defined(normalBam)
+            then runDir + "/results/variants/somaticSV.vcf.gz.tbi"
+            else runDir + "/results/variants/tumorSV.vcf.gz.tbi"
+        File? diploidSV = "/results/variants/diploidSV.vcf.gz"
+        File? diploidSVindex = "/results/variants/diploidSV.vcf.gz.tbi"
+    }
+
+    runtime {
+        cpu: cores
+        memory: memory
+    }
+}
\ No newline at end of file

strelka.wdl

@@ -34,7 +34,7 @@ task Germline {
 
         ~{runDir}/runWorkflow.py \
         -m local \
-        -J ~{cores} \
+        -j ~{cores} \
         -g ~{memory}
     }
 
@@ -62,6 +62,8 @@ task Somatic {
         File refFasta
         File? callRegions
         File? callRegionsIndex
+        File? indelCandidates
+        File? indelCandidatesIndex
         Boolean exome = false
 
         Int cores = 1
@@ -80,12 +82,13 @@ task Somatic {
         --tumorBam ~{tumorBam} \
         --ref ~{refFasta} \
         --runDir ~{runDir} \
-        ~{"--callRegions" + callRegions} \
+        ~{"--callRegions " + callRegions} \
+        ~{"--indelCandidates " + indelCandidates} \
         ~{true="--exome" false="" exome} \
 
         ~{runDir}/runWorkflow.py \
         -m local \
-        -J ~{cores} \
+        -j ~{cores} \
         -g ~{memory}
     }