pipeline/wdl/fusion.wdl

task rmdup_picard {
    String name
    String sorted_bam
    String output_dir
    String ref

    command <<<

        if [ ! -d ${output_dir}/fusion ];then
        mkdir ${output_dir}/fusion
        fi

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

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

}

task fusion_calling {
    String name
    String rmdup_bam
    String output_dir
    String ref
    String tumor_bamdst_depth
    String project

    command <<<

        if [ ! -d ${output_dir}/fusion ];then
        mkdir ${output_dir}/fusion
        fi

        # Extract the discordant paired-end alignments.
        samtools view -b -F 1294 ${rmdup_bam} > ${output_dir}/fusion/${name}.discordants.bam

        # Extract the split-read alignments
        samtools view -h ${rmdup_bam} \
        | /dataseq/jmdna/software/lumpy-sv/scripts/extractSplitReads_BwaMem -i stdin \
        | samtools view -Sb - \
        > ${output_dir}/fusion/${name}.splitters.bam

        lumpyexpress \
        -B ${rmdup_bam} \
        -S ${output_dir}/fusion/${name}.splitters.bam \
        -D ${output_dir}/fusion/${name}.discordants.bam \
        -o ${output_dir}/fusion/${name}.fusion.raw.vcf

        vcf_filter.py \
        -i ${output_dir}/fusion/${name}.fusion.raw.vcf \
        -e 'INFO/PE[0] >1 && INFO/SR[0] > 4 ' \
        | svtyper -B ${rmdup_bam} -T ${ref} -o ${output_dir}/fusion/${name}.fusion.vcf

        table_annovar.pl \
        ${output_dir}/fusion/${name}.fusion.vcf \
        /dataseq/jmdna/software/annovar/humandb/ \
        -buildver hg19 -nastring . -vcfinput -remove -otherinfo \
        -protocol refGene \
        -operation g \
        -outfile ${output_dir}/fusion/${name}.fusion

        filter_fusion.pl ${tumor_bamdst_depth} \
        ${output_dir}/fusion/${name}.fusion.hg19_multianno.vcf \
        ${output_dir}/fusion/${name}.fusion.hg19_multianno.filter.txt \
        ${project}

        filter_longindel.pl ${output_dir}/fusion/${name}.fusion.hg19_multianno.vcf  \
        ${output_dir}/fusion/${name}.longindel.hg19_multianno.filter.txt ${project}

    >>>

    output {
        String fusion_filter_txt = "${output_dir}/fusion/${name}.fusion.hg19_multianno.filter.txt"
        String longindel_filter_txt = "${output_dir}/fusion/${name}.longindel.hg19_multianno.filter.txt"
    }

}

task fusion_sum {
    String name
    String output_dir
    String fusion_filter_txt
    String longindel_filter_txt
    String cancer

    command <<<
        target_therapy_fusion.pl ${fusion_filter_txt} ${output_dir}/fusion/${name}.fusion.hg19_multianno.filter ${cancer}
        target_therapy_longindel.pl ${longindel_filter_txt} ${output_dir}/fusion/${name}.longindel.hg19_multianno.filter ${cancer}
    >>>
    output {
        String fusion_pos = "${output_dir}/fusion/${name}.fusion.hg19_multianno.filter.pos.txt"
        String longindel_pos = "${output_dir}/fusion/${name}.longindel.hg19_multianno.filter.pos.txt"
    }
}

workflow call_fusion {

    Boolean run=true

    String name
    String sorted_bam
    String rmdup_bam
    String output_dir
    String ref
    Boolean umi
    String tumor_bamdst_depth
    String project
    String cancer

    if (run) {
        if (umi) {
            call rmdup_picard {
                input:
                    name=name,
                    sorted_bam=sorted_bam,
                    output_dir=output_dir,
                    ref=ref
            }
            call fusion_calling as fusion_calling_umi {
                input:
                    name=name,
                    rmdup_bam=rmdup_picard.rmdup_bam,
                    output_dir=output_dir,
                    ref=ref,
                    tumor_bamdst_depth=tumor_bamdst_depth,
                    project=project
            }
            call fusion_sum as fusion_sum_umi {
                input:
                    fusion_filter_txt=fusion_calling_umi.fusion_filter_txt,
                    longindel_filter_txt=fusion_calling_umi.longindel_filter_txt,
                    name=name,
                    output_dir=output_dir,
                    cancer=cancer

            }

        }

        if (!umi) {
            call fusion_calling as fusion_calling {
                input:
                    name=name,
                    rmdup_bam=rmdup_bam,
                    output_dir=output_dir,
                    ref=ref,
                    tumor_bamdst_depth=tumor_bamdst_depth,
                    project=project
            }
            call fusion_sum as fusion_sum {
                input:
                    fusion_filter_txt=fusion_calling.fusion_filter_txt,
                    longindel_filter_txt=fusion_calling.longindel_filter_txt,
                    name=name,
                    output_dir=output_dir,
                    cancer=cancer

            }
        }
    }

    output {
        String fusion_vcf = "${output_dir}/fusion/${name}.fusion.vcf"
        String fusion_pos = "${output_dir}/fusion/${name}.fusion.hg19_multianno.filter.pos.txt"
        String longindel_pos = "${output_dir}/fusion/${name}.longindel.hg19_multianno.filter.pos.txt"
    }
}