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Fix annotate delly output arg #48

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merged 3 commits into from
Mar 20, 2024
Merged

Fix annotate delly output arg #48

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d68f9dd
Add --output arg
ryanjameskennedy Mar 20, 2024
35b7009
Update CHANGELOG.md re annotate-delly --output arg
ryanjameskennedy Mar 20, 2024
0ad389c
Add --version arg
ryanjameskennedy Mar 20, 2024
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,8 @@

### Fixed

- Fixed `--output` arg re annotate delly

### Changed

- Removed sample id from Sample object
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7 changes: 6 additions & 1 deletion prp/cli.py
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Original file line number Diff line number Diff line change
@@ -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
Expand Down Expand Up @@ -48,6 +50,7 @@


@click.group()
@click.version_option(__version__)
def cli():
"""Jasen pipeline result processing tool."""

Expand Down Expand Up @@ -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)
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