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)