pipeline/wdl/msi.wdl

# msi

task run_msi {
    String name
    String probe
    String output_dir
    String tumor_rmdup_bam
    String normal_rmdup_bam

    command <<<
        if [ ! -d ${output_dir}/msi ];then
        mkdir ${output_dir}/msi
        fi

        if [ "${probe}" == "682" ]; then

        echo "msi 682探针 "
        msisensor2 msi \
        -f 0.01 \
        -d /dataseq/jmdna/software/msisensor2/msi.10-50.homosite.list \
        -n ${normal_rmdup_bam} -t ${tumor_rmdup_bam} \
        -e $PUBLIC/msi/624_650_intersect_depth50_177.bed \
        -b 10 -c 30 -o ${output_dir}/msi/${name}.msi.txt

        elif [ "${probe}" == "624" ]; then

        echo "msi 624 探针 "
        msisensor2 msi \
        -M /dataseq/jmdna/software/msisensor2/models_hg19_GRCh37 \
        -t ${tumor_rmdup_bam} -e $PUBLIC/msi//624_650_intersect_depth50_177.bed -b 10 \
        -o ${output_dir}/msi/${name}.msi.txt

        elif [ "${probe}" == "160" ]; then

        echo "msi 160 探针 "
        msisensor2 msi \
        -M /dataseq/jmdna/software/msisensor2/models_hg19_GRCh37 \
        -t ${tumor_rmdup_bam} -e $PUBLIC/msi/624_650_160_intersect_74.bed \
        -b 10 ${output_dir}/msi/${name}.msi.txt

        else
        echo "未知的选项: ${probe}"
        fi

    >>>

}

workflow call_msi {
    Boolean run=true

    String probe
    String tumor
    String tumor_rmdup_bam
    String? normal_rmdup_bam
    String output_dir

    if (run) {

        call run_msi {
            input:
                name=tumor,
                probe=probe,
                output_dir=output_dir,
                tumor_rmdup_bam=tumor_rmdup_bam,
                normal_rmdup_bam=normal_rmdup_bam
        }
    }

    output {
        String msi_txt = "${output_dir}/msi/${tumor}.msi.txt"
    }
}