pipeline/wdl/chemo.wdl

# chemo

task run_chemo {
    String name
    String output_dir
    String probe
    String vcf
    String cancer
    String project
    String bam
    String ref
    command {
        if [ ! -d ${output_dir}/chemo ];then
        mkdir ${output_dir}/chemo
        fi

        chemo.py -d $DATABASE/chemo_database.xlsx -probe ${probe} -n ${name} -v ${vcf} -o ${output_dir}/chemo -c ${cancer} -p ${project} -b ${bam} -r ${ref}

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

workflow call_chemo {

    Boolean run=true

    String name
    String? normal
    String output_dir
    String probe
    String vcf
    String cancer
    String project
    String tumor_rmdup_bam
    String? normal_rmdup_bam
    String ref

    if (run) {
        if (defined(normal)) {
            call run_chemo as  run_chemo_normal {
                input:
                    name=name,
                    output_dir=output_dir,
                    probe=probe,
                    vcf=vcf,
                    cancer=cancer,
                    project=project,
                    bam=normal_rmdup_bam,
                    ref=ref
            }
        }
        if (!defined(normal)) {
            call run_chemo as run_chemo_tumor {
                input:
                    name=name,
                    output_dir=output_dir,
                    probe=probe,
                    vcf=vcf,
                    cancer=cancer,
                    project=project,
                    bam=tumor_rmdup_bam,
                    ref=ref
            }
        }

    }

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