java -jar cromwell.jar run strelkaSomatic.wdl --inputs inputs.json

 	set -eo pipefail
 
 	~{writeBed}
 	~{indexFeatureFile}
 
 	configureStrelkaSomaticWorkflow.py \
 	--normalBam ~{normalBam} \
 	--tumorBam ~{tumorBam} \
 	--referenceFasta ~{refFasta} \
 	~{regionsBedArg} \
 	--runDir .
 
 	./runWorkflow.py -m local -j ~{threads}

         python3 <<CODE
         import os, re
         intervalFiles = re.split(",", "~{sep=',' intervalFiles}")
         for intervalFile in intervalFiles:
             items = re.split("\.", os.path.basename(intervalFile))
             items.pop() # remove .interval_list suffix
             bedName = ".".join(items)+".bed"
             with open(intervalFile, 'r') as inFile, open(bedName, 'w') as outFile:
                 for line in inFile:
                     if not re.match("@", line): # omit the GATK header
                         fields = re.split("\t", line.strip())
                         fields[1] = str(int(fields[1]) - 1)
                         outFile.write("\t".join(fields)+"\n")
         CODE

 	set -eo pipefail
 
 	mkdir interval-files
 	ln -s ~{refFai}
 	ln -s ~{refDict}
 	~{gatk} --java-options "-Xmx~{memory-8}g" SplitIntervals \
 	-R ~{refFasta} \
 	~{intervalsArg} \
 	~{scatterArg} \
 	--subdivision-mode BALANCING_WITHOUT_INTERVAL_SUBDIVISION \
 	-O interval-files \
 	~{splitIntervalsExtraArgs}
 
 	cp interval-files/*.interval_list .

    set -eo pipefail
 
    ~{gatk} GatherVcfs \
    -I ~{sep=" -I " vcfs} \
    -R ~{refFasta}
    -O ~{outputName}
 
    gzip ~{outputName}