[ont-qc] Add .pdf file into ng6 analysis for nanopore runs
The pdf file would be in the same location than the jflow and the log file. So into /work/sbsuser/data/Nanopore/RUN_REP/jflow. It would be named report.pdf
The pdf file would be in the same location than the jflow and the log file. So into /work/sbsuser/data/Nanopore/RUN_REP/jflow. It would be named report.pdf
added New feature label
Talked about it to @mmanno
mentioned in commit 07725731
So it did not work, investigation is happening!
mentioned in commit eaeee36f
Problem is : the path to retrieve logs is based on the working directory and this is different from the folder where are the fastq files and logs.
So : little modification in the code
# 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(logpath+"/*.log"):
self.log_files.append(file)
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))
closed
changed milestone to %V3.2.6