fusioncatcher/tasks/fusioncatcher.wdl

task fusioncatcher{
	String sample_id
	File sample_fastq_dir
	File database_dir
	
	String docker
	String cluster
	String disk_size

	command <<<
	
	set -o pipefail
	set -e

	mkdir -p ${sample_id}/output


	/software/fusioncatcher/bin/fusioncatcher \
	-d ${database_dir} \
	-p 4 \
	--input ${sample_fastq_dir} \
	--output ${sample_id}/output

	>>>
	
	runtime {
	docker :  docker
	cluster: cluster
	systemDisk: "cloud_ssd 40"
	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
	}

	output {
	Array[File] fusioncatcher_result=glob("${sample_id}/output/*")
	}

}