fix somatic tasks and add supporting tasks

Created by: DavyCats

strelka.wdl

 version 1.0
 
+task Germline {
+    input {
+        String? preCommand
+        String? installDir
+        String runDir
+        Array[File]+ bams
+        Array[File]+ indexes
+        File refFasta
+        File refFastaIndex
+        File? callRegions
+        File? callRegionsIndex
+        Boolean exome = false
+        Boolean rna = false
+
+        Int cores = 1
+        Int memory = 4
+    }
+
+    String toolCommand = if defined(installDir)
+        then installDir + "bin/configureStrelkaGermlineWorkflow.py"
+        else "configureStrelkaGermlineWorkflow.py"
+
+    command {
+        set -e -o pipefail
+        ~{preCommand}
+        ~{toolCommand} \
+        --bam ~{sep=" --bam " bams} \
+        --ref ~{refFasta} \
+        --runDir ~{runDir} \
+        ~{"--callRegions " + callRegions} \
+        ~{true="--exome" false="" exome} \
+        ~{true="--rna" false="" rna}
+
+        ~{runDir}/runWorkflow.py \
+        -m local \
+        -j ~{cores} \
+        -g ~{memory}
+    }
+
+    output {
+        File variants = runDir + "/results/variants/variants.vcf.gz"
+        File variantsIndex = runDir + "/results/variants/variants.vcf.gz.tbi"
+    }
+
+    runtime {
+        cpu: cores
+        memory: memory
+    }
+}
+
+
 task Somatic {
     input {
         String? preCommand
         String? installDir
         String runDir
         File normalBam
+        File normalIndex
         File tumorBam
+        File tumorIndex
         File refFasta
+        File refFastaIndex
+        File? callRegions
+        File? callRegionsIndex
+        File? indelCandidates
+        File? indelCandidatesIndex
+        Boolean exome = false
 
         Int cores = 1
         Int memory = 4
@@ -24,11 +83,14 @@ task Somatic {
         --normalBam ~{normalBam} \
         --tumorBam ~{tumorBam} \
         --ref ~{refFasta} \
-        --runDir ~{runDir}
+        --runDir ~{runDir} \
+        ~{"--callRegions " + callRegions} \
+        ~{"--indelCandidates " + indelCandidates} \
+        ~{true="--exome" false="" exome} \
 
         ~{runDir}/runWorkflow.py \
         -m local \
-        -J ~{cores} \
+        -j ~{cores} \
         -g ~{memory}
     }