def krakenAlignContig(infile, outfile): #set memory and threads job_memory = str(PARAMS["Kraken_memory"]) + "G" job_threads = int(PARAMS["Kraken_threads"]) #generate call to diamond statement = PipelineAnnotate.runKraken( infile, outfile, PARAMS, "{}scripts/translateKraken2.py".format( os.path.dirname(__file__).rstrip("pipelines"))) P.run(statement)
def krakenAlignContig(infile, outfile): #set memory and threads job_memory = str(PARAMS["Kraken_memory"]) + "G" job_threads = int(PARAMS["Kraken_threads"]) #generate call to diamond statementlist = [ PipelineAnnotate.runKraken( infile, outfile.replace(".gz", ""), PARAMS, "{}scripts/translateKraken2.py".format( os.path.dirname(__file__).rstrip("pipelines"))) ] #compress outputs statementlist.append("gzip {}".format( outfile.replace("translated.gz", "out"))) statementlist.append("gzip {}".format(outfile.replace(".gz", ""))) statement = " && ".join(statementlist) P.run(statement)