65 lines
1.5 KiB
Plaintext
65 lines
1.5 KiB
Plaintext
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task run_pollution {
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String name
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String output_dir
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String probe
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String vcf
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String? vcf2
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command <<<
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if [ ! -d ${output_dir}/pollution ];then
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mkdir ${output_dir}/pollution
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fi
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pollution.py -n ${name} \
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-v ${vcf} \
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-v2 ${vcf2} \
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-o ${output_dir}/pollution \
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-p ${probe} \
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-b $PUBLIC/pollution/${probe}_contaminate_ref.bed \
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-c $PUBLIC/pollution/${probe}_contaminate_cnvkit.bed
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>>>
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output {
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String pollution_res = "${output_dir}/pollution/${name}_pollution.csv"
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}
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}
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workflow call_pollution {
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Boolean run=true
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String tumor
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String? normal
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String output_dir
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String probe
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String raw_vcf
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String somatic_vcf
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String germline_vcf
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if (run) {
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if (defined(normal)) {
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call run_pollution as run_pollution_paired {
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input:
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name=tumor,
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output_dir=output_dir,
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probe=probe,
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vcf=somatic_vcf,
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vcf2=germline_vcf
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}
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}
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if (!defined(normal)) {
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call run_pollution as run_pollution_single {
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input:
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name=tumor,
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output_dir=output_dir,
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probe=probe,
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vcf=raw_vcf
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}
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}
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}
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output {
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String pollution_res = "${output_dir}/pollution/${name}_pollution.csv"
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}
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}
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