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 ${sample_id}/input/
        mkdir -p ${sample_id}/output/
        cp ${fastq1} ${sample_id}/input/
        cp ${fastq2} ${sample_id}/input/

        /software/fusioncatcher/bin/fusioncatcher \
            -d ${database_dir} \
            -p 4 \
            --input ${sample_id}/input \
            --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("${sample_id}/output/*.txt")
        Array[File] fusioncatcher_zip=glob("${sample_id}/output/*.zip")
        Array[File] fusioncatcher_log=glob("${sample_id}/output/*.log")
        Array[File] fusioncatcher_vcf=glob("${sample_id}/output/*.vcf")
    }

}