[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

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