bug

codes/run_wdl.py

@@ -9,6 +9,7 @@ import time
 from datetime import datetime
 
 import pandas as pd
+import requests
 
 
 def get_branch_nodes(graph, start_node):
@@ -62,6 +63,17 @@ def get_catecode(project, start_node='addQc'):
     return cate_dict
 
 
+def send_ding(msg):
+    '''
+    发送钉钉消息功能
+    '''
+    url = 'https://oapi.dingtalk.com/robot/send?access_token=d4a0749cc7ff87bd12079a79dd74ca3423becb1ce161c3088acc6628a7a188dd'
+    data = {"msgtype": "text", "text": {"content": "pipeline:" + str(msg)}, "at": {"isAtAll": True}}
+    headers = {'Content-Type': 'application/json;charset=UTF-8'}
+    send_data = json.dumps(data).encode('utf-8')
+    ret = requests.post(url=url, data=send_data, headers=headers)
+
+
 def run(barcode, normal, umi, input_dir, output_dir, project, cancer, probe, wdl, start_node):
     input_dir = os.path.realpath(input_dir)
     output_dir = os.path.realpath(output_dir)
@@ -108,6 +120,8 @@ def run(barcode, normal, umi, input_dir, output_dir, project, cancer, probe, wdl
     output, error = ret.communicate()
     print(output, error)
 
+    send_ding(msg=f'样本{barcode}已开始分析，分析地址\n{output_dir}')
+
     stdout = open(os.path.join(output_dir, f'{args.barcode}_{logname}_stdout.log'), 'w')
     stderr = open(os.path.join(output_dir, f'{args.barcode}_{logname}_stderr.log'), 'w')
 
@@ -159,6 +173,7 @@ def run(barcode, normal, umi, input_dir, output_dir, project, cancer, probe, wdl
             stderr.write(file_path + '\n')
             stderr.write(f.read())
             stderr.write('\n\n')
+    send_ding(msg=f'样本{barcode}已分析完成，分析地址\n{output_dir}, 请查看！')
     stdout.close()
     stderr.close()
 

wdl/msi.wdl

@@ -36,7 +36,7 @@ task run_msi {
         msisensor2 msi \
         -M /dataseq/jmdna/software/msisensor2/models_hg19_GRCh37 \
         -t ${tumor_rmdup_bam} -e $PUBLIC/msi/624_650_160_intersect_74.bed \
-        -b 10 ${output_dir}/msi/${name}.msi.txt
+        -b 10 -o ${output_dir}/msi/${name}.msi.txt
 
         else
         echo "未知的选项: ${probe}"