diff --git a/vamb/__main__.py b/vamb/__main__.py index ff5bf8d7..7cc320f1 100755 --- a/vamb/__main__.py +++ b/vamb/__main__.py @@ -1611,7 +1611,7 @@ def add_help_arguments(parser: argparse.ArgumentParser): def add_general_arguments(subparser: argparse.ArgumentParser): add_help_arguments(subparser) - reqos = subparser.add_argument_group(title="Output (required)", description=None) + reqos = subparser.add_argument_group(title="Output", description=None) reqos.add_argument( "--outdir", metavar="", @@ -1639,10 +1639,7 @@ def add_general_arguments(subparser: argparse.ArgumentParser): metavar="", type=int, default=DEFAULT_THREADS, - help=( - "number of threads to use when parsing BAM" - "[min(" + str(DEFAULT_THREADS) + ", nbamfiles)]" - ), + help=f"number of threads to use where customizable [{DEFAULT_THREADS}]", ) general.add_argument( "--norefcheck", @@ -1926,8 +1923,8 @@ def add_clustering_arguments(subparser): dest="max_clusters", metavar="", type=int, - default=None, - help="stop after c clusters [None = infinite]", + default=None, # meaning: do not stop + help=argparse.SUPPRESS, ) return subparser @@ -2068,7 +2065,7 @@ def main(): Version: {vamb.__version_str__} Default use, good for most datasets: - vamb bin default --outdir out --fasta my_contigs.fna --bamdir bam_dir -o C + vamb bin default --outdir out --fasta my_contigs.fna --bamdir bam_dir Find the latest updates and documentation at https://github.com/RasmussenLab/vamb""" logger.add(sys.stderr, format=format_log)