更新qcfail

codes/postprocess.py

@@ -91,6 +91,7 @@ class PostProcess:
         # 突变的等级分类
         if '证据等级' in df.columns:
             df['AMP_mut_level'] = df['证据等级'].replace(['A', 'B', 'C', 'D'], ['I', 'I', 'II', 'II'])
+            # df['NCCN_mut_level'] = df['证据等级'].replace(['A', 'B', 'C', 'D'], ['I', 'II', 'II', 'II'])
 
         # 药物等级划分
         if 'Response_Type_C' in df.columns and '证据等级' in df.columns:
@@ -527,7 +528,8 @@ class PostProcess:
         if qc_files:
             if os.path.getsize(qc_files[0]) > 0:
                 qc = pd.read_csv(qc_files[0], sep='\t', header=None)
-                qc_res = [qc.set_index(0)[1].to_dict()]
+                qc_content = qc.set_index(0)[1].to_dict()
+                qc_res = [qc_content]
         self.sheet['qc'] = qc_res
 
     def drugs(self):

codes/run_wdl.py

@@ -66,12 +66,13 @@ def get_catecode(project, start_node='addQc'):
     return cate_dict
 
 
-def send_ding(msg):
+def send_ding(msg, isat=True):
     '''
     发送钉钉消息功能
     '''
     url = 'https://oapi.dingtalk.com/robot/send?access_token=0c4b2dc1b6a1b459826512cc27adbd14e4f6aa2e661b7a7c284669065bbccfc5'
-    data = {"msgtype": "text", "text": {"content": "pipeline:" + str(msg)}, "at": {"isAtAll": True}}
+    # url = 'https://oapi.dingtalk.com/robot/send?access_token=d4a0749cc7ff87bd12079a79dd74ca3423becb1ce161c3088acc6628a7a188dd'
+    data = {"msgtype": "text", "text": {"content": "pipeline:" + str(msg)}, "at": {"isAtAll": isat}}
     headers = {'Content-Type': 'application/json;charset=UTF-8'}
     send_data = json.dumps(data).encode('utf-8')
     session.post(url=url, data=send_data, headers=headers)
@@ -116,7 +117,7 @@ def run(barcode, normal, umi, input_dir, output_dir, project, cancer, probe, wdl
     # 记录开始时间
     start_time = time.time()
     if not debug:
-        send_ding(msg=f'\n样本: {barcode}\n分析地址: \n{output_dir} \n 开始分析')
+        send_ding(msg=f'\n样本: {barcode}\n分析地址: \n{output_dir} \n 开始分析', isat=False)
     ret = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE, encoding="utf-8")
     pidnum = ret.pid
     with open(os.path.join(output_dir, 'pid'), 'w') as pidfile:
@@ -163,12 +164,12 @@ def run(barcode, normal, umi, input_dir, output_dir, project, cancer, probe, wdl
     # 按照文件的修改时间倒序排序
     sorted_stdout_files = sorted(stdout_files, key=lambda x: os.path.getmtime(x), reverse=True)
     sorted_stderr_files = sorted(stderr_files, key=lambda x: os.path.getmtime(x), reverse=True)
-
     for file_path in sorted_stdout_files:
         with open(file_path, 'r') as f:
             stdout.write('#' * 50 + '\n')
             stdout.write(file_path + '\n')
-            stdout.write(f.read())
+            f_read = f.read()
+            stdout.write(f_read)
             stdout.write('\n\n')
 
     for file_path in sorted_stderr_files:
@@ -177,8 +178,18 @@ 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')
+
+    qcfail_f = os.path.join(output_dir, 'report', f'{barcode}_qcfail.txt')
+    if os.path.exists(qcfail_f):
+        with open(qcfail_f, "r") as qcfail_f_out:
+            qcfail = qcfail_f_out.read()
+    else:
+        qcfail = '流程失败，请核查！！！'
+    if not qcfail:
+        qcfail = '合格'
     if not debug:
-        send_ding(msg=f'\n样本: {barcode}\n分析地址: \n{output_dir} \n 分析完成，请查看！')
+        send_ding(msg=f'\n样本: {barcode}\n分析地址: \n{output_dir} \n 分析完成，请查看！\n\n qcfail: \n {qcfail}\n')
+
     stdout.close()
     stderr.close()
 

wdl/postprocess.wdl

@@ -22,6 +22,7 @@ task run_post {
         fi
         indication.pl ${output_dir} ${cancer} ${project}
         sample_post.py -s ${name} -o ${output_dir}
+        qc_check.py -n ${output_dir}/qc/${name}_qc.txt -s ${output_dir}/qc/${normal}_qc.txt -p ${output_dir}/pollution/${name}_gender_res.txt -c ${output_dir}/qc/${name}_post.json -o ${output_dir}/report/${name}_qcfail.txt
         postprocess.py -n ${name} -s ${normal} -c ${output_dir} -o ${output_dir}/report/${name}.merged_file.xlsx
 
     }