性别鉴定

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)) {