#alignment

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

    command <<<
        if [ ! -d ${output_dir}/alignment ];then
        mkdir ${output_dir}/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 ${output_dir}/alignment/${name}.sorted.bam
        samtools index ${output_dir}/alignment/${name}.sorted.bam

    >>>

    output {
        String sorted_bam = "${output_dir}/alignment/${name}.sorted.bam"
    }
}

#remove PCR duplicates

task markduplicates_genecore {
    String name
    String ref
    String sorted_bam
    String output_dir

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

        gencore -i ${sorted_bam} \
        -o ${output_dir}/alignment/${name}.rmdup.bam \
        -r ${ref} \
        -u UMI \
        -j ${output_dir}/alignment/${name}_rmdup.json \
        -h ${output_dir}/alignment/${name}_rmdup.html

        samtools index ${output_dir}/alignment/${name}.rmdup.bam
    >>>

    output {
        String rmdup_bam = "${output_dir}/alignment/${name}.rmdup.bam"
    }
}

task markduplicates_picard {
    String name
    String ref
    String sorted_bam
    String output_dir

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

        java -XX:+UseParallelGC -XX:ParallelGCThreads=8 -Xmx12G  -jar $PICARD MarkDuplicates \
        I=${sorted_bam} \
        O=${output_dir}/alignment/${name}.rmdup.bam  \
        CREATE_INDEX=true \
        M=${output_dir}/alignment/${name}.rmdup.metrics.txt  \
        R=${ref}

    >>>

    output {
        String rmdup_bam = "${output_dir}/alignment/${name}.rmdup.bam"
    }
}

# generater mpileup file

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

    command <<<

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

    >>>

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

workflow alignment {

    String tumor
    String tumor_r1
    String tumor_r2

    String? normal
    String? normal_r1
    String? normal_r2

    Boolean umi

    String ref
    String bed
    String output_dir

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

            }
            if (name==tumor) {
                if (umi) {
                    call markduplicates_genecore as tumor_markduplicates_genecore {
                        input:
                            name=name,
                            ref=ref,
                            output_dir=output_dir,
                            sorted_bam=bwa.sorted_bam,
                    }
                }
                if (!umi) {
                    call markduplicates_picard as tumor_markduplicates_picard {
                        input:
                            name=name,
                            ref=ref,
                            output_dir=output_dir,
                            sorted_bam=bwa.sorted_bam,
                    }
                }
            }

            if (name==select_first([normal, 'None'])) {
                call markduplicates_picard as normal_markduplicates_picard {
                    input:
                        name=name,
                        ref=ref,
                        output_dir=output_dir,
                        sorted_bam=bwa.sorted_bam,
                }
            }

        }
    }

    output {
        String tumor_sorted_bam = "${output_dir}/alignment/${tumor}.sorted.bam"
        String tumor_rmdup_bam = "${output_dir}/alignment/${tumor}.rmdup.bam"
        String tumor_pileup = "${output_dir}/alignment/${tumor}.pileup"
        String normal_sorted_bam = "${output_dir}/alignment/${normal}.sorted.bam"
        String normal_rmdup_bam = "${output_dir}/alignment/${normal}.rmdup.bam"
        String normal_pileup = "${output_dir}/alignment/${normal}.pileup"
    }
}