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

    }

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

workflow call_tmb {

    Boolean run=true

    String name
    String file
    String project
    String output_dir
    Boolean umi

    if (run) {
        call run_tmb {
            input:
                name=name,
                file=file,
                project=project,
                sample_type=if umi then 'c' else 't',
                output_dir=output_dir
        }

    }

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