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perf: Update Datavzrd wrapper #3122

Merged
merged 2 commits into from
Aug 21, 2024
Merged

perf: Update Datavzrd wrapper #3122

merged 2 commits into from
Aug 21, 2024

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fxwiegand
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@fxwiegand fxwiegand commented Aug 20, 2024

QC

While the contributions guidelines are more extensive, please particularly ensure that:

  • test.py was updated to call any added or updated example rules in a Snakefile
  • input: and output: file paths in the rules can be chosen arbitrarily
  • wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in input: or output:)
  • 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
  • the meta.yaml contains a link to the documentation of the respective tool or command under url:
  • conda environments use a minimal amount of channels and packages, in recommended ordering

Summary by CodeRabbit

  • New Features

    • Updated the datavzrd package to the latest version, potentially enhancing performance and adding new functionalities.
  • Bug Fixes

    • Upgrading to the new version may resolve existing issues from the prior version.

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coderabbitai bot commented Aug 20, 2024

Walkthrough

The primary change involves updating the version of the datavzrd dependency in the environment.yaml file from 2.41.1 to 2.41.2. This update may enhance the project by introducing bug fixes, performance improvements, or new features associated with the latest version of the package. The specific implications of this change will depend on the actual updates in the datavzrd package.

Changes

Files Change Summary
utils/datavzrd/environment.yaml Updated datavzrd version from 2.41.1 to 2.41.2

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Actionable comments posted: 0

Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between 62b0231 and a26bd62.

Files selected for processing (1)
  • utils/datavzrd/environment.yaml (1 hunks)
Additional comments not posted (1)
utils/datavzrd/environment.yaml (1)

5-5: Verify compatibility with other dependencies.

The datavzrd version has been updated to 2.41.2. Ensure that this version is compatible with other dependencies in the environment, especially yte =1.5.4.

@johanneskoester johanneskoester merged commit 5101461 into master Aug 21, 2024
6 checks passed
@johanneskoester johanneskoester deleted the fxwiegand-patch-1 branch August 21, 2024 08:52
johanneskoester pushed a commit that referenced this pull request Aug 21, 2024
🤖 I have created a release \*beep\* \*boop\*
---
##
[4.1.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v4.0.0...v4.1.0)
(2024-08-21)


### Features

* Allow outputting of rendered yte config in Datavzrd wrapper
([#3123](https://www.github.com/snakemake/snakemake-wrappers/issues/3123))
([e74be78](https://www.github.com/snakemake/snakemake-wrappers/commit/e74be7843299478a276febfacb52825a9762500c))


### Bug Fixes

* Correctly handle non str index list for bwa-mem2/mem
([#3101](https://www.github.com/snakemake/snakemake-wrappers/issues/3101))
([6f46508](https://www.github.com/snakemake/snakemake-wrappers/commit/6f46508aa99663930e70c82114205929aee2dfcb))


### Performance Improvements

* autobump bio/gatk3/baserecalibrator
([#3119](https://www.github.com/snakemake/snakemake-wrappers/issues/3119))
([6c2bdfd](https://www.github.com/snakemake/snakemake-wrappers/commit/6c2bdfdca79c7037448bc601a4aeb3d578ea0980))
* autobump bio/gatk3/realignertargetcreator
([#3118](https://www.github.com/snakemake/snakemake-wrappers/issues/3118))
([ba219e7](https://www.github.com/snakemake/snakemake-wrappers/commit/ba219e7698eb078fe22c703a9662c8cb6deee0eb))
* autobump bio/genomescope
([#3117](https://www.github.com/snakemake/snakemake-wrappers/issues/3117))
([6292229](https://www.github.com/snakemake/snakemake-wrappers/commit/62922298404397c7b23dc5b8fb01bc33e445e97f))
* autobump bio/igv-reports
([#3120](https://www.github.com/snakemake/snakemake-wrappers/issues/3120))
([fe33c2c](https://www.github.com/snakemake/snakemake-wrappers/commit/fe33c2c27328212c528e94f995fd0bc26d7fde39))
* autobump bio/trinity
([#3121](https://www.github.com/snakemake/snakemake-wrappers/issues/3121))
([62b0231](https://www.github.com/snakemake/snakemake-wrappers/commit/62b0231c99920200e3fa6794f87578869cc35bd5))
* Update Datavzrd wrapper
([#3122](https://www.github.com/snakemake/snakemake-wrappers/issues/3122))
([5101461](https://www.github.com/snakemake/snakemake-wrappers/commit/51014613939bfc5e48e0b2ae619e283cf36bfd88))
---


This PR was generated with [Release
Please](https://github.com/googleapis/release-please). See
[documentation](https://github.com/googleapis/release-please#release-please).

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
@coderabbitai coderabbitai bot mentioned this pull request Sep 16, 2024
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