task runqc {
    String name
    String inputDir
    String outputDir

    command <<<
        echo "###### ${name} fastp beginning at: $(date) ######"

        if [ ! -d ${outputDir}/qc ];then
        mkdir ${outputDir}/qc
        fi

        fastp -i ${inputDir}/*_$name_*1.fq.gz -o ${outputDir}/qc/${name}_clean_R1.fq.gz \
        -I ${inputDir}/*_$name_*2.fq.gz -O ${outputDir}/qc/${name}_clean_R2.fq.gz \
        -w 10 \
        --correction \
        --overlap_len_require 10 \
        -j ${outputDir}/qc/${name}.json \
        -h ${outputDir}/qc/${name}.html \
        --report_title $name \
        -e 20

        echo "###### ${name} fastp end at: $(date) ######"
    >>>
    output {
        String r1 = "${outputDir}/qc/${name}_clean_R1.fq.gz "
        String r2 = "${outputDir}/qc/${name}_clean_R2.fq.gz "
        String json = "${outputDir}/qc/${name}.json"
    }

}

workflow qc {

    String tumor
    String? normal
    String inputDir
    String outputDir

    scatter(name in [tumor, normal]) {
        if (defined(name)) {
            call runqc {
                input:
                    name=name,
                    inputDir=inputDir,
                    outputDir=outputDir
            }
        }
    }

    output {
        String tumor_r1 = "${outputDir}/qc/${tumor}_clean_R1.fq.gz "
        String tumor_r2 = "${outputDir}/qc/${tumor}_clean_R2.fq.gz "
        String tumor_json = "${outputDir}/qc/${tumor}.json"
        String normal_r1 = "${outputDir}/qc/${normal}_clean_R1.fq.gz "
        String normal_r2 = "${outputDir}/qc/${normal}_clean_R2.fq.gz "
        String normal_json = "${outputDir}/qc/${normal}.json"
    }
}