From cd859b95be7d7b42e8a573e5fe8b0a0e02b48b0e Mon Sep 17 00:00:00 2001 From: Amandine PERRIN <amandine.perrin@pasteur.fr> Date: Wed, 4 Dec 2019 09:34:50 +0100 Subject: [PATCH] Output dir required with only-mash option --- PanACoTA/subcommands/prepare.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/PanACoTA/subcommands/prepare.py b/PanACoTA/subcommands/prepare.py index ddc057da..5aebd0fe 100644 --- a/PanACoTA/subcommands/prepare.py +++ b/PanACoTA/subcommands/prepare.py @@ -395,10 +395,13 @@ def check_args(parser, args): if args.no_refseq and not args.outdir: parser.error("You must provide an output directory, where your results will be saved.") - # If user wants only mash steps, check that he gave info file + # If user wants only mash steps, check that he gave info file, and outdir if args.only_mash and not args.from_info: parser.error("If you want to run only Mash filtering steps, please give the " "info file with the required information (see '--info' option)") + if args.only_mash and not args.outdir: + parser.error("If you want to run only Mash filtering steps, please give the " + "output directory where you want to save your results (see '-o' option)") # Cannot be verbose and quiet at the same time if args.verbose > 0 and args.quiet: -- GitLab