[ont_qc>__init__]

Logs are retrieved from the path of fastq files, and not on the working
directory

workflows/ont_qc/__init__.py

@@ -54,20 +54,17 @@ class OntQualityCheck (NG6Workflow):
         logging.getLogger("jflow").debug("OntQualityCheck.process! sample_name : "+str(sample_names))
         logging.getLogger("jflow").debug("OntQualityCheck.process! summary_file : "+str(self.summary_file))
         
-        ### check for log file
-        # get current path
-        cmd = [self.get_exec_path("pwd")]
-        p = Popen(cmd, stdout=PIPE, stderr=PIPE)
-        stdout, stderr = p.communicate()
-        exec_path = stdout.decode("utf-8").rsplit()[0]
-        logging.getLogger("jflow").debug("OntQualityCheck._process.logfile pwd = " + str(exec_path))
+        ### check for log file self.fastq_files
+        # get the dirname of reads folder, logs are in this dirname/jflow/
+        logpath = os.path.dirname( self.get_all_reads()[0] ) + "/jflow/"
+        logging.getLogger("jflow").debug("OntQualityCheck._process.logfile logpath = " + logpath)
+        
         # find .log files
-        for file in glob(exec_path+"/*.log"):
+        for file in glob(logpath+"/*.log"):
             self.log_files.append(file)
-        for file in glob(exec_path+"/*.pdf"):
+        for file in glob(logpath+"/*.pdf"):
             self.log_files.append(file)
         logging.getLogger("jflow").debug("OntQualityCheck._process.logfile self.log_files = " + ",".join(self.log_files))
-        logging.getLogger("jflow").debug("OntQualityCheck._process.logfile exiting")
         
         # add logs
         if len(self.log_files) > 0 :
@@ -81,4 +78,7 @@ class OntQualityCheck (NG6Workflow):
             trim_porechop = self.add_component("Trim_porechop", [self.get_all_reads() , "discard_middle"])
         if self.fast5dir != None:
             fast5archive = self.add_component("Fast5archive", [self.fast5dir, "fast5archive.tar"])
+        
+        logging.getLogger("jflow").debug("OntQualityCheck._process.logfile exiting")
+        
 

[Audrey Gibert]

#131 (closed) is involved!