fusioncatcher/tasks/fusioncatcher.wdl

task fusioncatcher{
    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 /cromwell_root/input/
        mkdir -p /cromwell_root/output/
        cp ${fastq1} /cromwell_root/input/
        cp ${fastq2} /cromwell_root/input/

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

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

    output {
        Array[File] fusioncatcher_result=glob("/cromwell_root/output/*.txt")
        Array[File] fusioncatcher_zip=glob("/cromwell_root/output/*.zip")
        Array[File] fusioncatcher_log=glob("/cromwell_root/output/*.log")
        Array[File] fusioncatcher_vcf=glob("/cromwell_root/output/*.vcf")
    }

}