pipeline/wdl/postprocess.wdl

task run_post {
    String?  mutation
    String? fusion
    String? cnv
    String?  msi
    String? hereditary
    String? chemo
    String? pollution
    String name
    String? normal
    String output_dir
    String cancer
    command <<<

        if [ ! -d ${output_dir}/report ];then
        mkdir ${output_dir}/report
        fi
        indication.pl ${output_dir} ${cancer}
        sample_post.py -s ${normal} -o ${output_dir}
        postprocess.py -n ${name} -s ${normal} -c ${output_dir} -o ${output_dir}/report/${name}.merged_file.xlsx
    >>>

    output {
        String merged = "${output_dir}/report/${name}.merged_file.xlsx"
    }
}

workflow call_postprocess {

    Boolean run=true

    String?  mutation
    String? fusion
    String? cnv
    String? msi
    String? hereditary
    String? pollution
    String? chemo
    String name
    String? normal
    String output_dir
    String cancer

    if (run) {
        call run_post {
            input:
                mutation=mutation,
                fusion=fusion,
                cnv=cnv,
                msi=msi,
                hereditary=hereditary,
                chemo=chemo,
                pollution=pollution,
                name=name,
                normal=normal,
                output_dir=output_dir,
                cancer=cancer
        }
    }

    output {
        String merged = "${output_dir}/report/${name}.merged_file.xlsx"
    }
}