From db1c34a59f5c729b0abf1c95c02d03a43c20de06 Mon Sep 17 00:00:00 2001
From: chaopower <chao.zhang@jmdna.com>
Date: Wed, 31 Jan 2024 17:32:39 +0800
Subject: [PATCH] =?UTF-8?q?=E6=80=A7=E5=88=AB=E9=89=B4=E5=AE=9A?=
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---
 wdl/pollution.wdl | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

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)) {