From 820e0afaa26b907508de339596460b5183718651 Mon Sep 17 00:00:00 2001 From: Ryan Routsong Date: Fri, 12 Jan 2024 09:41:38 -0700 Subject: [PATCH] fix: add actual help messages to argparse arguments --- weave | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/weave b/weave index 681fbf5..95af79b 100755 --- a/weave +++ b/weave @@ -88,37 +88,37 @@ if __name__ == '__main__': parser_run = sub_parsers.add_parser('run', formatter_class=argparse.RawTextHelpFormatter, epilog=utils.get_alias_table()) parser_run.add_argument('rundir', metavar='', nargs="+", type=utils.valid_run_input, - help='Full & complete run id (format YYMMDD_INSTRUMENTID_TIME_FLOWCELLID) or absolute paths') + help='Full & complete run id (format YYMMDD_INSTRUMENTID_TIME_FLOWCELLID) or absolute paths.') parser_run.add_argument('-s', '--seq_dir', metavar='', default=None, type=str, help='Root directory for sequencing data (defaults for biowulf/bigsky/locus), must contain directories ' + \ 'matching run ids, if not using full paths.') parser_run.add_argument('-o', '--output', metavar='', default=None, type=str, - help='Top-level output directory for demultiplexing data (defaults to input directory + runid + "_demux")') + help='Top-level output directory for demultiplexing data (defaults to input directory + runid + "_demux").') parser_run.add_argument('-d', '--dry-run', action='store_true', - help='Dry run the demultiplexing workflow') + help='Dry run the demultiplexing workflow.') parser_run.add_argument('-n', '--noqc', action='store_false', - help='Do not run the QC/QA portion of the workflow (Default is on)') + help='Do not run the QC/QA portion of the workflow (Default is on).') parser_run.add_argument('--sheetname', metavar='Sample Sheet Filename', - help='Name of the sample sheet file to look for (default is SampleSheet.csv)') + help='Name of the sample sheet file to look for (default is SampleSheet.csv).') parser_run.add_argument('-l', '--local', action='store_true', - help='Execute pipeline locally without a dispatching executor') + help='Execute pipeline locally without a dispatching executor.') # disambiguate arguments parser_run.add_argument('-t', '--host', type=files.valid_fasta, default=None, - help='Execute pipeline locally without a dispatching executor.') + help='Full path to host genome for disambiguate to use or short name genome alias.') parser_run.add_argument('-p', '--pathogen', type=files.valid_fasta, default=None, - help='Execute pipeline locally without a dispatching executor.') + help='Full path to pathogen/graft/parasite genome for disambiguate to use or short name genome alias.') parser_cache = sub_parsers.add_parser('cache') parser_cache.add_argument('cachedir', metavar='', type=cache.valid_dir, - help='Relative or absolute path to directory for cache storage') + help='Relative or absolute path to directory for cache storage.') parser_cache.add_argument('-l', '--local', action='store_true', help='Execute pipeline locally without a dispatching executor') parser_unlock = sub_parsers.add_parser('unlock') parser_unlock.add_argument('unlockdir', metavar='', type=cache.valid_dir, - help='Relative or absolute path to directory for cache storage') + help='Full path to directory to unlock.') parser_run.set_defaults(func = run) parser_cache.set_defaults(func = get_cache)