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"
    }
}

task run_tmb_umi {
    String name
    String file
    String project
    String sample_type
    String output_dir
    String tumor_rmdup_bam

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

        correct_umi_overlap_reads.py ${output_dir}/tmb/${name}.tmb.pre.txt ${tumor_rmdup_bam} ${output_dir}/tmb/${name}.tmb.txt


    }

    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
    String tumor_rmdup_bam

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


    }

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