pipeline/wdl/chemo.wdl

task run_chemo {
    String name
    String output_dir
    String probe
    String vcf
    String cancer
    String project
    command <<<

        if [ ! -d ${output_dir}/chemo ];then
        mkdir ${output_dir}/chemo
        fi
        chemo.py -probe ${probe} -n ${name} -v ${vcf} -o ${output_dir}/chemo -c ${cancer} -p ${project}
    >>>

    output {
        String chemo_res = "${output_dir}/chemo/${name}.drug.res.txt"
    }
}

workflow call_chemo {

    Boolean run=true

    String name
    String output_dir
    String probe
    String vcf
    String cancer
    String project

    if (run) {
        call run_chemo {
            input:
                name=name,
                output_dir=output_dir,
                probe=probe,
                vcf=vcf,
                cancer=cancer,
                project=project
        }
    }

    output {
        String chemo_res = "${output_dir}/chemo/${name}.drug.res.txt"
    }
}