def main(argv):
# set recommended java heap settings
os.environ['NXF_OPTS'] = '-Xms1g -Xmx4g'
args, unknown = parse(argv)
logfile = os.path.join(args.tracedir[0], args.logfile[0])
profile = ','.join(args.profile)
script = args.script[0] if not args.revision else args.script[0] + " -r %s" % args.revision[0]
reportdir = args.tracedir[0]
utils.create_report_dir(reportdir)
reads = args.reads[0]
command = "nextflow -log %s run %s " % (logfile, script)
command += "-profile %s --genome %s --tracedir %s " % ( profile, args.genome[0], reportdir)
# Check for glob files and reads in awsbatch
if (reads.startswith('s3://')):
print("Replacing --reads by readPaths")
s3bucket, globPattern = os.path.split(reads)
readPathsConfig = convertToReadPathsConfig(filesGlob=globPattern, bucket=s3bucket)
command += "-c %s " % readPathsConfig
else:
command += "--reads %s " % reads
command += ' '.join(unknown)
run(command=command, script=script, tracedir=reportdir, dryrun=args.dryrun)
def main(argv):
args = parse(argv)
aws_queue = args.awsqueue
out_dir = args.outDir
work = args.work
script = args.script_location
nextflow_args = args.nextflow_args if args.nextflow_args else ''
local_report_dir = args.localReportDir
logfile = args.logfile
dry_run = args.dryrun
resume = '-resume' if args.resume else ''
profile = ','.join(args.profile)
genome = args.genome
genome_base = args.genome_base
# locate the logfile in the localReportDir
logfile = os.path.join(local_report_dir, logfile)
utils.create_report_dir(local_report_dir)
run_multiqc(aws_queue=aws_queue,
profile=profile,
out_dir=out_dir,
work_dir=work,
script=script,
resume=resume,
nextflow_args=nextflow_args,
local_report_dir=local_report_dir,
logfile=logfile,
genome=genome,
genome_base=genome_base,
dry_run=dry_run)
def main(argv):
args = parse(argv)
aws_queue = args.awsqueue
out_base = args.outDir
work_base = args.work
script = args.script_location
genome = args.genome
genome_base = args.genome_base
nextflow_args = args.nextflow_args if args.nextflow_args else ''
tools = args.tools
local_report_dir = args.localReportDir
logfile = args.logfile
dry_run = args.dryrun
resume = '-resume' if args.resume else ''
samples = args.samples
# locate the logfile in the localReportDir
logfile = os.path.join(local_report_dir, logfile)
utils.create_report_dir(local_report_dir)
# if only one sample.tsv given don't change work/out dir
if len(samples) > 1 and type(samples) == list:
for sample in samples:
# create a work and output folder path for each sample
sample_id = utils.get_simple_basename(sample)
out_dir = os.path.join(out_base, sample_id)
work = os.path.join(work_base, sample_id)
run_sample(tsv_file=sample, aws_queue=aws_queue, tools=tools, out_dir=out_dir, work=work, script=script,
genome=genome, genome_base=genome_base, resume=resume, nextflow_args=nextflow_args,
local_report_dir=local_report_dir, dry_run=dry_run, logfile=logfile)
elif len(samples) == 1 and type(samples) == list:
sample = samples[0]
out_dir = out_base
work = work_base
run_sample(tsv_file=sample, aws_queue=aws_queue, tools=tools, out_dir=out_dir, work=work, script=script,
genome=genome, genome_base=genome_base, resume=resume, nextflow_args=nextflow_args,
local_report_dir=local_report_dir, logfile=logfile, dry_run=dry_run)
else:
sys.stderr.write('Found %i samples. Could not resolve sample: \'%s\'' % (samples, len(samples)))
sys.exit(1)
def main(argv):
args = parse(argv)
aws_queue = args.awsqueue
out_dir = args.outDir
work = args.work
script = args.script_location
genome = args.genome
genome_base = args.genome_base
nextflow_args = args.nextflow_args if args.nextflow_args else ''
annotate_tools = '--annotateTools %s' % args.annotateTools if args.annotateTools else ''
tools = args.tools
local_report_dir = args.localReportDir
logfile = args.logfile
dry_run = args.dryrun
resume = '-resume' if args.resume else ''
profile = ','.join(args.profile)
# locate the logfile in the localReportDir
logfile = os.path.join(local_report_dir, logfile)
utils.create_report_dir(local_report_dir)
try:
annotate_sample(aws_queue=aws_queue,
profile=profile,
annotate_tools=annotate_tools,
tools=tools,
out_dir=out_dir,
work=work,
script=script,
genome=genome,
genome_base=genome_base,
resume=resume,
nextflow_args=nextflow_args,
local_report_dir=local_report_dir,
logfile=logfile,
dry_run=dry_run)
except RuntimeError as err:
raise err