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

    }
}

workflow call_pollution {

    Boolean run=true

    String tumor
    String? normal
    String output_dir
    String probe
    String raw_vcf
    String somatic_vcf
    String germline_vcf

    if (run) {
        if (defined(normal)) {
            call run_pollution as run_pollution_paired {
                input:
                    name=tumor,
                    output_dir=output_dir,
                    probe=probe,
                    vcf=somatic_vcf,
                    vcf2=germline_vcf
            }
        }

        if (!defined(normal)) {
            call run_pollution as run_pollution_single {
                input:
                    name=tumor,
                    output_dir=output_dir,
                    probe=probe,
                    vcf=raw_vcf
            }
        }
    }

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