pipeline/wdl/msi.wdl

# msi

task msi_single {
    String name
    String bed
    String output_dir
    String rmdup_bam

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

        msisensor2 msi \
        -M /dataseq/jmdna/software/msisensor2/models_hg19_GRCh37 \
        -t ${output_dir}/alignment/${name}.rmdup.bam \
        -e ${bed} \
        -b 10 \
        -o ${output_dir}/msi/${name}.msi.txt
    >>>

    output {
        String run_msi_txt = "${output_dir}/msi/${name}.msi.txt"
    }
}

task msi_paired {
    String bed
    String name
    String output_dir
    String tumor_rmdup_bam
    String normal_rmdup_bam

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

        msisensor2 msi \
        -d /dataseq/jmdna/software/msisensor2/hg19.microsatellites.list \
        -n ${normal_rmdup_bam} \
        -t ${tumor_rmdup_bam} \
        -e ${bed} \
        -b 10 \
        -o ${output_dir}/msi/${name}.msi.txt

    >>>

    output {
        String run_msi_txt = "${output_dir}/msi/${name}.msi.txt"
    }

}

workflow call_msi {
    Boolean run=true

    String tumor
    String tumor_rmdup_bam
    String? normal
    String? normal_rmdup_bam
    String bed
    String output_dir

    if (run) {
        # 单样本
        if (!defined(normal)) {
            call msi_single {
                input:
                    name=tumor,
                    output_dir=output_dir,
                    rmdup_bam=tumor_rmdup_bam,
                    bed=bed
            }
        }
        # 双样本
        if (defined(normal)) {
            call msi_paired {
                input:
                    name=tumor,
                    bed=bed,
                    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"
    }
}