Comments (3)
I could replace the match_on
argument with a more general wildcard_name
argument, which would allow the user to specify "sample_id"
, "tumour_id"
, or "normal_id"
.
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@BrunoGrandePhD I implemented it into some of my modules and pushed the edit to master. Would the new edits be installed using pip install oncopipe
or do users have to use pip install -e lcr-modules/oncopipe
?
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I created a new release on GitHub (v1.0.7), which automatically deploys to PyPI.
https://github.com/LCR-BCCRC/lcr-modules/releases
https://pypi.org/project/oncopipe/
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Related Issues (20)
- Liftover issue regarding seq_type HOT 1
- SAGE doesn't handle `chr` prefixes correctly HOT 9
- StringTie HOT 1
- Oncopipe mis-handling unmatched normal IDs HOT 1
- Add unmatched samples to demo data HOT 1
- Update documentation HOT 1
- Documenting what each tool accomplishes
- Default unmatched normal bug HOT 2
- Harmonize all CNV caller modules and automatically convert seg files to projections HOT 2
- in_module is missing from some output rules
- Refactor the LymphGen module to run per-sample HOT 1
- Missing lymphgen script HOT 4
- Mutect2 edge case error HOT 2
- finalizing seg files have an issue with special genome builds HOT 3
- Ecotyper module needs wget conda environment HOT 2
- QC module does not report the per-chromosome coverage
- Lofreq- no INDEL calling HOT 2
- ancient flag on all samples tsv prevents rerun of gistic2 HOT 1
- Strelka SomaticEVS filtering threshold HOT 2
- Demo doesn't dry-run as documented HOT 2
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