pipeline/wdl/tmb.wdl

# tmb

task run_tmb {
    String name
    String file
    String project
    String sample_type
    String output_dir

    command <<<

        if [ ! -d ${output_dir}/tmb ];then
        mkdir ${output_dir}/tmb
        fi
        filter_snpindel.pl \
        ${file} \
        ${output_dir}/tmb/${name}.tmb.txt \
        ${output_dir}/tmb/${name}.tmb.tag.txt \
        ${project} \
        ${sample_type} \
        tmb
    >>>

}

workflow call_tmb {

    Boolean run=true

    String name
    String file
    String project
    String output_dir
    Boolean umi

    if (run) {
        if (umi) {
            call run_tmb as run_tmb_umi {
                input:
                    name=name,
                    file=file,
                    project=project,
                    sample_type='c',
                    output_dir=output_dir
            }
        }
        if (!umi) {
            call run_tmb as run_tmb_tissue {
                input:
                    name=name,
                    file=file,
                    project=project,
                    sample_type='t',
                    output_dir=output_dir
            }

        }

    }

    output {
        String tmb_txt = "${output_dir}/tmb/${name}.tmb.txt"
    }
}