#alignment

task bwa {
    String name
    String read1
    String read2
    String outputDir
    String ref

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

        bwa mem -R '@RG\tID:group_n\tLB:library_n\tPL:BGI\tPU:unit1\tSM:${name}' -M -t 10 ${ref} ${read1} ${read2} | \
        samtools view -@ 10 -bh  -o - | samtools sort -@ 10  -o ${outputDir}/alignment/${name}.sorted.bam
        samtools index ${outputDir}/alignment/${name}.sorted.bam

    >>>

    output {
        String sortedBam = "${outputDir}/alignment/${name}.sorted.bam"
    }
}

#remove PCR duplicates

task markduplicates {
    String name
    String ref
    String sortedBam
    String outputDir

    command <<<
        if [ ! -d ${outputDir}/alignment ];then
        mkdir ${outputDir}/alignment
        fi
        java -XX:+UseParallelGC -XX:ParallelGCThreads=2 -Xmx12G  -jar $PICARD MarkDuplicates \
        I=${sortedBam} \
        O=${outputDir}/alignment/${name}.rmdup.bam  \
        CREATE_INDEX=true \
        M=${outputDir}/alignment/${name}.rmdup.metrics.txt  \
        R=${ref}

    >>>

    output {
        String rmdupBam = "${outputDir}/alignment/${name}.rmdup.bam"
    }
}

# generater mpileup file

task generater_mpileup {
    String name
    String rmdupBam
    String ref
    String bed
    String outputDir

    command <<<

        samtools mpileup -Bq 20 -Q 20  -f ${ref} -l ${bed} ${rmdupBam} -o ${outputDir}/alignment/${name}.pileup

    >>>

    output {
        String pileup = "${outputDir}/alignment/${name}.pileup"
    }
}

workflow alignment {

    String tumor
    String tumor_r1
    String tumor_r2

    String? normal
    String? normal_r1
    String? normal_r2

    String ref
    String bed
    String outputDir

    scatter(name in [tumor, normal]) {
        if (defined(name)) {
            call bwa {
                input:
                    name=name,
                    ref=ref,
                    outputDir=outputDir,
                    read1=if name==tumor then tumor_r1 else normal_r1,
                    read2=if name==tumor then tumor_r2 else normal_r2

            }
            call markduplicates {
                input:
                    name=name,
                    ref=ref,
                    outputDir=outputDir,
                    sortedBam=bwa.sortedBam
            }
            call generater_mpileup {
                input:
                    name=name,
                    ref=ref,
                    outputDir=outputDir,
                    bed=bed,
                    rmdupBam=markduplicates.rmdupBam
            }

        }
    }

    output {
        String tumor_sortedBam = "${outputDir}/alignment/${tumor}.sorted.bam"
        String tumor_rmdupBam = "${outputDir}/alignment/${tumor}.rmdup.bam"
        String tumor_pileup = "${outputDir}/alignment/${tumor}.pileup"
        String normal_sortedBam = "${outputDir}/alignment/${normal}.sorted.bam"
        String normal_rmdupBam = "${outputDir}/alignment/${normal}.rmdup.bam"
        String normal_pileup = "${outputDir}/alignment/${normal}.pileup"
    }
}