Merge pull request #2 from treangenlab/update_my_recipe

remove metavar="" to avoid assertion error
treangenlab · May 10, 2023 · 4142726 · 4142726
2 parents a2f9842 + dd015a5
commit 4142726
Showing 1 changed file with 5 additions and 5 deletions.
diff --git a/meth_phaser_parallel b/meth_phaser_parallel
@@ -26,39 +26,39 @@ def parse_arg(argv):
  type=str,
  help="input methylation annotated bam file",
  required=True,
- metavar="",
+ # metavar="",
  )
  required_args.add_argument(
  "-r",
  "--reference",
  type=str,
  help="reference genome",
  required=True,
- metavar="",
+ # metavar="",
  )
  required_args.add_argument(
  "-g",
  "--gtf",
  type=str,
  help="gtf file from whatshap visualization",
  required=True,
- metavar="",
+ # metavar="",
  )
  required_args.add_argument(
  "-vc",
  "--vcf_called",
  type=str,
  help="called vcf file from HapCUT2",
  required=True,
- metavar="",
+ # metavar="",
  )
  parser.add_argument(
  "-vt",
  "--vcf_truth",
  type=str,
  help="Truth vcf file for benchmarking",
  default=None,
- metavar="",
+ # metavar="",
  )
  parser.add_argument(
  "-t", "--threads", type=int, help="threads", default=1, metavar=""