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/*")
    }

}