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 cnv = "${output_dir}/msi/${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 cnv = "${output_dir}/msi/${name}.msi.txt"
    }

}

workflow call_msi {

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

    # 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 cnv = "${output_dir}/msi/${tumor}.msi.txt"
    }
}