Merge pull request #48 from Clinical-Genomics-Lund/fix-annotate-delly…

…-output-arg

Fix annotate delly output arg

CHANGELOG.md

@@ -8,6 +8,8 @@
 
 ### Fixed
 
+ - Fixed `--output` arg re annotate delly
+
 ### Changed
 
  - Removed sample id from Sample object

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."""
 
@@ -416,7 +419,9 @@ 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)