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src/a/r/ARC-HEAD/ARC/runners/mapper.py   ARC(Download)
            if PEs + SEs > 0:
                checker_params['targets'][target_dir] = False
                self.submit(Assembler.to_job(assembly_params))
 
        logger.info("------------------------------------")
        if len(checker_params['targets']) > 0:
            # checker = AssemblyChecker(checker_params)
            self.submit(AssemblyChecker.to_job(checker_params))
        else:
            logger.info("Sample: %s No reads mapped, no more work to do." % checker_params['sample'])

src/a/r/ARC-HEAD/ARC/runners/assembly_checker.py   ARC(Download)
            # checker = AssemblyChecker(checker_params)
            time.sleep(5)  # sleep 5 seconds before putting a checker back on the job_q
            self.submit(AssemblyChecker.to_job(checker_params))
            logger.info("Sample: %s Assemblies not finished: %s of %s targets completed" % (sample, completed, len(self.params['targets'])))
        else:
            # finisher = Finisher(params)
            logger.debug("Sample: %s, iteration %s, Submitting finisher job to queue." % (sample, self.params['iteration']))
            self.submit(Finisher.to_job(params))
            logger.info("Sample: %s Assemblies finished: %s of %s targets completed" % (sample, completed, len(self.params['targets'])))
 

src/a/r/ARC-HEAD/ARC/runners/finisher.py   ARC(Download)
            del mapper_params['targets']
            mapper_params['reference'] = os.path.join(self.params['working_dir'], 'I%03d' % self.params['iteration'] + '_contigs.fasta')
            self.submit(Mapper.to_job(mapper_params))
            logger.info("Sample: %s Added new mapper to queue: iteration %s" % (self.params['sample'], self.params['iteration']))