Varscan/Snpeff wrappers are incompatible - please add warning to documentation #275
Comments
|
i write, here too (other post here). any news on the topic? |
|
I am not familiar with |
|
This issue was marked as stale because it has been open for 6 months with no activity. |
johanneskoester
added a commit
that referenced
this issue
Feb 3, 2025
<!-- Ensure that the PR title follows conventional commit style (<type>: <description>)--> <!-- Possible types are here: https://github.com/commitizen/conventional-commit-types/blob/master/index.json --> <!-- Add a description of your PR here--> I have been contacted about issue #275 . Varscan2 and SnpEff are compatible while calling somatic variants. No error is produced, and SNP are correctly annotated in the end. ### QC <!-- Make sure that you can tick the boxes below. --> * [X] I confirm that I have followed the [documentation for contributing to `snakemake-wrappers`](https://snakemake-wrappers.readthedocs.io/en/stable/contributing.html). While the contributions guidelines are more extensive, please particularly ensure that: * [X] `test.py` was updated to call any added or updated example rules in a `Snakefile` * [X] `input:` and `output:` file paths in the rules can be chosen arbitrarily * [X] wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in `input:` or `output:`) * [X] temporary files are either written to a unique hidden folder in the working directory, or (better) stored where the Python function `tempfile.gettempdir()` points to * [X] the `meta.yaml` contains a link to the documentation of the respective tool or command under `url:` * [X] conda environments use a minimal amount of channels and packages, in recommended ordering <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **New Features** - Introduced a structured meta-wrapper configuration for a bioinformatics pipeline detailing variant calling and annotation steps. - Added a new Snakefile that outlines a comprehensive workflow for genomic variant analysis, integrating multiple tools. - Updated the used wrappers file to include new bioinformatics tools for enhanced functionality. - **Tests** - Added a new test function to verify the integration of VarScan2 with SnpEff for variant annotation. <!-- end of auto-generated comment: release notes by coderabbit.ai --> --------- Co-authored-by: tdayris <[email protected]> Co-authored-by: tdayris <[email protected]> Co-authored-by: Johannes Köster <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com> Co-authored-by: Felix Mölder <[email protected]> Co-authored-by: Christopher Schröder <[email protected]> Co-authored-by: Filipe G. Vieira <[email protected]>
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
When running the two snakemake wrappers
Varscan->SnpEffin succession there is an error thrown pcingola/SnpEff#267 (comment)This does not happen when feeding
Varscanto theVEPannotation tool.This should be mentioned on the docs: https://snakemake-wrappers.readthedocs.io/en/stable/wrappers/varscan.html
The text was updated successfully, but these errors were encountered: