From d68f9ddb95f1766d938daeb5b23a00dba69180a6 Mon Sep 17 00:00:00 2001 From: ryanjameskennedy Date: Wed, 20 Mar 2024 12:14:51 +0100 Subject: [PATCH 1/3] Add --output arg --- prp/cli.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/prp/cli.py b/prp/cli.py index 87a586f..436c2ef 100644 --- a/prp/cli.py +++ b/prp/cli.py @@ -416,7 +416,9 @@ def create_qc_result(sample_id, bam, bed, baits, reference, cpus, output) -> Non @cli.command() @click.option("-v", "--vcf", type=click.Path(exists=True), help="VCF file") @click.option("-b", "--bed", type=click.Path(exists=True), help="BED file") -@click.argument("output", type=click.Path(writable=True)) +@click.option( + "-o", "--output", required=True, type=click.File("w"), help="output filepath" +) def annotate_delly(vcf, bed, output): """Annotate Delly SV varinats with genes in BED file.""" output = Path(output) From 35b70095fd80e2393b839d1cd0eec53e230ab150 Mon Sep 17 00:00:00 2001 From: ryanjameskennedy Date: Wed, 20 Mar 2024 12:21:49 +0100 Subject: [PATCH 2/3] Update CHANGELOG.md re annotate-delly --output arg --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index ce3e775..b672989 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,6 +8,8 @@ ### Fixed + - Fixed `--output` arg re annotate delly + ### Changed - Removed sample id from Sample object From 0ad389c33f5b3e2cb49ac6a32863e605b0579529 Mon Sep 17 00:00:00 2001 From: ryanjameskennedy Date: Wed, 20 Mar 2024 12:56:47 +0100 Subject: [PATCH 3/3] Add --version arg --- prp/cli.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/prp/cli.py b/prp/cli.py index 436c2ef..1a4bb19 100644 --- a/prp/cli.py +++ b/prp/cli.py @@ -1,4 +1,6 @@ """Definition of the PRP command-line interface.""" +from prp import VERSION as __version__ + import json import logging from pathlib import Path @@ -48,6 +50,7 @@ @click.group() +@click.version_option(__version__) def cli(): """Jasen pipeline result processing tool."""