starfusion/tasks/starfusion.wdl

task starfusion{
	String sample_id
	File fastq1
	File fastq2
	File database_dir
	
	String docker
	String cluster
	String disk_size

	command <<<
	
	set -o pipefail
	set -e

	mkdir -p ${sample_id}/output

	STAR-Fusion --genome_lib_dir ${database_dir} \
        --left_fq ${fastq1} \
        --right_fq ${fastq2} \
        --CPU 4 \
        --output_dir  ${sample_id}/output
	>>>
	
	runtime {
	docker :  docker
	cluster: cluster
        systemDisk: "cloud_ssd 40"
        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
	}

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

}