96 lines
2.5 KiB
Plaintext
Executable File
96 lines
2.5 KiB
Plaintext
Executable File
# pollution
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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 cnvkit_tumor_vcf = "${output_dir}/pollution/${name}_cnvkit_tumor.vcf"
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String cnvkit_normal_vcf = "${output_dir}/pollution/${name}_cnvkit_normal.vcf"
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}
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}
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task run_generate_png {
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String name
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String probe
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String cnvkit_tumor_vcf
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String cnvkit_normal_vcf
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String cnv_cnr
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String cnv_cns
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String output_dir
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command {
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cnvkit.py scatter ${cnv_cnr} -s ${cnv_cns} -v ${cnvkit_tumor_vcf} -o ${output_dir}/pollution/${name}_pollution_cnvkit_tumor.png
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cnvkit.py scatter ${cnv_cnr} -s ${cnv_cns} -v ${cnvkit_normal_vcf} -o ${output_dir}/pollution/${name}_pollution_cnvkit_normal.png
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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 initial_vcf
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String normal_vcf
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String cnv_cnr
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String cnv_cns
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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=initial_vcf,
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vcf2=normal_vcf
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}
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call run_generate_png {
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input:
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name=tumor,
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probe=probe,
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cnvkit_tumor_vcf=run_pollution_paired.cnvkit_tumor_vcf,
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cnvkit_normal_vcf=run_pollution_paired.cnvkit_normal_vcf,
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cnv_cnr=cnv_cnr,
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cnv_cns=cnv_cns,
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output_dir=output_dir
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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=initial_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 = "${output_dir}/pollution/${tumor}_pollution.txt"
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}
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} |