fix: help genome alias table and remote cache assets

config/remote.json

@@ -1,6 +1,8 @@
 {
     "bcl2fastq": "docker://umccr/bcl2fastq:latest",
     "weave": "docker://rroutsong/weave_ngsqc:0.0.1",
+    "bclconvert": "docker://rroutsong/weave_bclconvert:0.0.3",
+    "disambiguate": "docker://quay.io/biocontainers/ngs-disambiguate:2018.05.03--hf393df8_7",
     "kraken": "https://genome-idx.s3.amazonaws.com/kraken/k2_pluspfp_16gb_20231009.tar.gz",
     "kaiju": "https://kaiju-idx.s3.eu-central-1.amazonaws.com/2023/kaiju_db_nr_euk_2023-05-10.tgz",
     "fastq_screen": "filelist://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/genome_locations.txt"

scripts/utils.py

@@ -8,6 +8,7 @@
 import os
 import yaml
 import sys
+import textwrap
 from argparse import ArgumentTypeError
 from dateutil.parser import parse as date_parser
 from subprocess import Popen, PIPE, STDOUT
@@ -41,8 +42,8 @@ def default(self, obj):
 
 
 def get_alias_table():
-    pp_tbl = lambda x: "\n".join([y.lstrip().rstrip() for y in x.split('\n')])
-    return pp_tbl("""+----------------+-------------------------------------------+
+    return textwrap.dedent("""Genome short name alias table:
+                     +----------------+-------------------------------------------+
                      | Organism       | Genomes supported (aka)                   |
                      +----------------+-------------------------------------------+
                      | HUMAN          | hg19(grch37) / hg38(grch38)               |

weave

@@ -83,10 +83,10 @@ def unlock_dir(sub_args):
 
 # ~~~~ argument parsing commands ~~~~
 if __name__ == '__main__':
-    main_parser = argparse.ArgumentParser(prog='weave')
+    main_parser = argparse.ArgumentParser(prog='weave', formatter_class=argparse.RawTextHelpFormatter, epilog=utils.get_alias_table())
     sub_parsers = main_parser.add_subparsers(help='run subcommand help')
 
-    parser_run = sub_parsers.add_parser('run')
+    parser_run = sub_parsers.add_parser('run', formatter_class=argparse.RawTextHelpFormatter, epilog=utils.get_alias_table())
     parser_run.add_argument('rundir', metavar='<run directory>', nargs="+", type=utils.valid_run_input, 
                             help='Full & complete run id (format YYMMDD_INSTRUMENTID_TIME_FLOWCELLID) or absolute paths')
     parser_run.add_argument('-s', '--seq_dir', metavar='<sequencing directory>', default=None, type=str,
@@ -106,9 +106,9 @@ if __name__ == '__main__':
     # disambiguate arguments
     parser_run.add_argument('-t', '--host', type=files.valid_fasta, default=None,
                         help='Execute pipeline locally without a dispatching executor.')
-    alias_table = "\n" + utils.get_alias_table() + "\n"
+
     parser_run.add_argument('-p', '--pathogen', type=files.valid_fasta, default=None,
-                        help='Execute pipeline locally without a dispatching executor. ' + alias_table)
+                        help='Execute pipeline locally without a dispatching executor.')
 
     parser_cache = sub_parsers.add_parser('cache')
     parser_cache.add_argument('cachedir', metavar='<cache directory>', type=cache.valid_dir,