pipeline/wdl/cnv.wdl

# cnv

task cnv_single {
    String name
    String output_dir
    String rmdup_bam
    String project
    String probe

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

        cnvkit.py batch ${rmdup_bam} \
        -r $PUBLIC/cnvkit/${probe}gene_pool_normal_reference.cnn \
        --drop-low-coverage  \
        --scatter \
        --diagram \
        --output-dir ${output_dir}/cnv \
        -p 5

        cnvkit.py scatter \
        ${output_dir}/cnv/${name}.rmdup.cnr -s ${output_dir}/cnv/${name}.rmdup.cns \
        --y-max 3 --y-min -3 \
        --title ${name}.cns \
        -o ${output_dir}/cnv/${name}.cnv.png

    >>>

    output {
        String cnv_cns = "${output_dir}/cnv/${name}.rmdup.cns"
    }
}

task cnv_paired {
    String name
    String ref
    String bed
    String output_dir
    String project
    String tumor_rmdup_bam
    String normal_rmdup_bam

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

        cnvkit.py batch \
        ${tumor_rmdup_bam} \
        --normal ${normal_rmdup_bam} \
        --targets ${bed} \
        --fasta ${ref} \
        --access $PUBLIC/cnvkit/access-5k-mappable.hg19.bed \
        --output-reference ${output_dir}/cnv/normal_reference.cnn \
        --annotate $PUBLIC/cnvkit/refFlat.txt \
        --drop-low-coverage \
        --scatter \
        --output-dir ${output_dir}/cnv \
        -p 5

        cnvkit.py scatter \
        ${output_dir}/cnv/${name}.rmdup.cnr -s ${output_dir}/cnv/${name}.rmdup.cns \
        --y-max 3 --y-min -3 \
        --title ${name}.cns \
        -o ${output_dir}/cnv/${name}.cnv.png

    >>>

    output {
        String cnv_cns = "${output_dir}/cnv/${name}.rmdup.cns"
    }

}

task cnv_sum {
    String cns
    String name
    String output_dir
    String project
    String cancer

    command <<<
        filter_cnv.pl ${cns} ${output_dir}/cnv/${name}.rmdup.cns.filter.txt ${project}
        target_therapy_cnv.pl ${output_dir}/cnv/${name}.rmdup.cns.filter.txt \
        ${output_dir}/cnv/${name}.rmdup.cns.filter ${cancer}
    >>>
    output {
        String cnv_filter = "${output_dir}/cnv/${name}.rmdup.cns.filter.txt"
    }
}

workflow call_cnv {

    Boolean run=true

    String tumor
    String tumor_rmdup_bam
    String? normal
    String? normal_rmdup_bam
    String ref
    String bed
    String output_dir
    String project
    String cancer
    String probe

    if (run) {
        # 单样本
        if (!defined(normal)) {
            call cnv_single {
                input:
                    name=tumor,
                    output_dir=output_dir,
                    rmdup_bam=tumor_rmdup_bam,
                    project=project,
                    probe=probe
            }
            call cnv_sum as cnv_single_sum {
                input:
                    cns=cnv_single.cnv_cns,
                    name=tumor,
                    output_dir=output_dir,
                    cancer=cancer,
                    project=project
            }
        }
        # 双样本
        if (defined(normal)) {
            call cnv_paired {
                input:
                    name=tumor,
                    ref=ref,
                    bed=bed,
                    output_dir=output_dir,
                    project=project,
                    tumor_rmdup_bam=tumor_rmdup_bam,
                    normal_rmdup_bam=normal_rmdup_bam
            }
            call cnv_sum as cnv_paired_sum {
                input:
                    cns=cnv_paired.cnv_cns,
                    name=tumor,
                    output_dir=output_dir,
                    cancer=cancer,
                    project=project
            }
        }
    }

    output {
        String cnv_filter = "${output_dir}/cnv/${tumor}.rmdup.cns.filter.txt"
    }
}