pipeline/wdl/pollution.wdl

# pollution

task run_pollution {
    String name
    String output_dir
    String probe
    String vcf
    String? vcf2

    command {

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

        pollution.py -n ${name} \
        -v ${vcf} \
        -v2 ${vcf2} \
        -o ${output_dir}/pollution \
        -p ${probe} \
        -b $PUBLIC/pollution/${probe}_contaminate_ref.bed \
        -c $PUBLIC/pollution/${probe}_contaminate_cnvkit.bed

    }
    output {
        String cnvkit_tumor_vcf = "${output_dir}/pollution/${name}_cnvkit_tumor.vcf"
        String cnvkit_normal_vcf = "${output_dir}/pollution/${name}_cnvkit_normal.vcf"
    }
}

task run_gender_dectec {
    String name
    String output_dir
    String probe
    String vcf
    String? vcf2

    command {

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

        gender_dectec.py -n ${name} -v ${vcf} -v2 ${vcf2} -o ${output_dir}/pollution -p ${probe} -g $PUBLIC/pollution/gender.bed

    }
}

task run_generate_png {
    String name
    String probe
    String cnvkit_tumor_vcf
    String cnvkit_normal_vcf
    String cnv_cnr
    String cnv_cns
    String output_dir

    command {
        cnvkit.py scatter ${cnv_cnr} -s ${cnv_cns} -v ${cnvkit_tumor_vcf} -o ${output_dir}/pollution/${name}_pollution_cnvkit_tumor.png
        cnvkit.py scatter ${cnv_cnr} -s ${cnv_cns} -v ${cnvkit_normal_vcf} -o ${output_dir}/pollution/${name}_pollution_cnvkit_normal.png
    }
}

task run_single_generate_png {
    String name
    String probe
    String cnvkit_tumor_vcf
    String cnv_cnr
    String cnv_cns
    String output_dir

    command {
        cnvkit.py scatter ${cnv_cnr} -s ${cnv_cns} -v ${cnvkit_tumor_vcf} -o ${output_dir}/pollution/${name}_pollution_cnvkit_tumor.png
    }
}

workflow call_pollution {

    Boolean run=true

    String tumor
    String? normal
    String output_dir
    String probe
    String raw_vcf
    String initial_vcf
    String normal_vcf
    String cnv_cnr
    String cnv_cns

    if (run) {
        if (defined(normal)) {
            call run_pollution as run_pollution_paired {
                input:
                    name=tumor,
                    output_dir=output_dir,
                    probe=probe,
                    vcf=initial_vcf,
                    vcf2=normal_vcf
            }
            call run_generate_png {
                input:
                    name=tumor,
                    probe=probe,
                    cnvkit_tumor_vcf=run_pollution_paired.cnvkit_tumor_vcf,
                    cnvkit_normal_vcf=run_pollution_paired.cnvkit_normal_vcf,
                    cnv_cnr=cnv_cnr,
                    cnv_cns=cnv_cns,
                    output_dir=output_dir

            }
            call run_gender_dectec {
                input:
                    name=tumor,
                    output_dir=output_dir,
                    probe=probe,
                    vcf=initial_vcf,
                    vcf2=normal_vcf
            }
        }

        if (!defined(normal)) {
            call run_pollution as run_pollution_single {
                input:
                    name=tumor,
                    output_dir=output_dir,
                    probe=probe,
                    vcf=initial_vcf
            }
            call run_single_generate_png {
                input:
                    name=tumor,
                    probe=probe,
                    cnvkit_tumor_vcf=run_pollution_single.cnvkit_tumor_vcf,
                    cnv_cnr=cnv_cnr,
                    cnv_cns=cnv_cns,
                    output_dir=output_dir

            }
        }
    }

    output {
        String pollution_res = "${output_dir}/pollution/${tumor}_pollution.txt"
    }
}