diff --git a/README.md b/README.md index 4277f570ac96166b15aca85870810968a6ebdb16..947346e65f5acdc2cb89815c30797b824832e4c8 100644 --- a/README.md +++ b/README.md @@ -155,9 +155,9 @@ Options: -ps, --positive-samples TEXT Sample(s) in positive-vcf to consider. May be called multiple times [required] -s, --stats PATH Path to output stats json file [required] - -dc, --discordant PATH Path to output the discordant VCF records to - --help Show this message and exit. -``` + -dc, --discordant PATH Path to output discordant VCF file + --help Show this message and exit + ``` ## License diff --git a/vtools/cli.py b/vtools/cli.py index 44a1d886ff191da9ea267b20aa2ad7ff969393a0..30cd698f6ea2a5811d578601798de07122a93d19 100644 --- a/vtools/cli.py +++ b/vtools/cli.py @@ -34,7 +34,7 @@ from .gcoverage import RefRecord, region_coverages @click.option("-s", "--stats", type=click.Path(writable=True), help="Path to output stats json file", required=True) @click.option("-dc", "--discordant", type=click.Path(writable=True), - help="Path to output the discordant VCF records to", + help="Path to output discordant VCF file", required=False) def evaluate_cli(call_vcf, positive_vcf, call_samples, positive_samples, stats, discordant):