Add --annotate flag to CNVKIT_BATCH
Open
@grantn5 is already working on this.
Since Oct 17, 2023.
enhancement
- Dominant language
- Nextflow
- Stars
- 429
- Forks
- 1.1k
- Avg merge
- 1d 6h
- Merged PRs (30d)
- 153
Description
Description of feature
Currently, the .cnn, .cns, and .cnr gene columns are not annotated by default as the cnvkit/batch module is missing the annotate argument.
chromosome start end gene log2 cn depth p_ttest probes weight
chr1 10000 248946422 - -0.137499 2 40.9002 0.338499 15 7.24467
chr2 10000 242183529 - -0.0943122 2 38.1783 0.301294 12 6.32129
chr3 10000 198235559 - 0.23336 3 46.2167 0.10641 8 2.7631
chr4 10000 190204555 - -0.25227 1 33.8353 0.256622 12 6.14349
chr5 10000 181478259 - -0.28567 1 32.5391 0.168916 18 4.91377
chr6 60000 170745979 - 0.0875944 2 43.6757 0.574441 7 4.48508
chr7 10000 159335973 - -0.224318 2 33.456 0.00531158 10 3.91519
chr8 60000 145078636 - 0.508863 3 55.382 0.00117615 6 4.90534
chr9 10000 138334717 - -0.292264 1 32.4998 3.85443e-05 33 5.56633
Ideally a pipeline input variable for cnvkit_annotation should be available to allow users to supply their refflat file.
See this link for a discussion of this issue on slack.
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Assessment
This issue has not been assessed yet.