diff --git a/wdl/pollution.wdl b/wdl/pollution.wdl index 38d6115..da2470b 100755 --- a/wdl/pollution.wdl +++ b/wdl/pollution.wdl @@ -12,6 +12,7 @@ task run_pollution { if [ ! -d ${output_dir}/pollution ];then mkdir ${output_dir}/pollution fi + pollution.py -n ${name} \ -v ${vcf} \ -v2 ${vcf2} \ @@ -27,6 +28,24 @@ task run_pollution { } } +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} -o ${output_dir}/pollution -p ${probe} -g $PUBLIC/pollution/gender.bed + + } +} + task run_generate_png { String name String probe @@ -77,6 +96,14 @@ workflow call_pollution { 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)) {