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perf: autobump bio/gatk3/realignertargetcreator #3118

Merged
merged 2 commits into from
Aug 16, 2024
Merged

perf: autobump bio/gatk3/realignertargetcreator #3118

merged 2 commits into from
Aug 16, 2024

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@snakedeploy-bot snakedeploy-bot bot commented Aug 16, 2024 •
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Automatic bump of bio/gatk3/realignertargetcreator.

Summary by CodeRabbit

  • New Features

    • Updated various packages and libraries in the conda environment to newer versions, enhancing overall performance and stability.
    • Incremented Python version from 3.12.4 to 3.12.5 for improved compatibility and security.

  • Bug Fixes

    • Upgraded OpenJDK, bzip2, c-ares, libdeflate, openssl, and R packages, which may include bug fixes and optimizations.

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coderabbitai bot commented Aug 16, 2024 •
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Walkthrough

The changes encompass updates to the configuration files for the bio/gatk3/realignertargetcreator module, focusing on dependency versions within the conda environment. Key updates include newer versions of the OpenJDK, bzip2, c-ares, libdeflate, openssl, and R packages, alongside a minor Python version increment. These modifications aim to enhance stability, performance, and security, ensuring compatibility with the latest features without introducing breaking changes.

Changes

Files Change Summary
bio/gatk3/realignertargetcreator/environment.linux-64.pin.txt
bio/gatk3/realignertargetcreator/environment.yaml		 Updated multiple package versions, including OpenJDK, bzip2, c-ares, libdeflate, and openssl, along with an increment of Python from 3.12.4 to 3.12.5.

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mergify[bot]
mergify bot approved these changes Aug 16, 2024
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Automatically approving successfull autobump

coderabbitai[bot]
coderabbitai bot reviewed Aug 16, 2024
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Actionable comments posted: 0

Review details

Configuration used: CodeRabbit UI
Review profile: ASSERTIVE

Commits

Files that changed from the base of the PR and between 6f46508 and ba8ddf0.

Files selected for processing (2)
  • bio/gatk3/realignertargetcreator/environment.linux-64.pin.txt (6 hunks)
  • bio/gatk3/realignertargetcreator/environment.yaml (1 hunks)
Additional comments not posted (2)
bio/gatk3/realignertargetcreator/environment.yaml (1)

7-7: Python version updated to 3.12.5.

The update from 3.12.4 to 3.12.5 is a minor version change, likely for bug fixes or security improvements.

Ensure compatibility with other dependencies in the environment.

bio/gatk3/realignertargetcreator/environment.linux-64.pin.txt (1)

Line range hint 16-142: Multiple package version updates.

The updates include OpenJDK, bzip2, c-ares, libdeflate, openssl, R packages, and others. These changes are aimed at improving stability, performance, and security.

Ensure that these updates do not introduce compatibility issues and verify the functionality of the updated environment.

@mergify mergify bot merged commit ba219e7 into master Aug 16, 2024
7 checks passed
@mergify mergify bot deleted the autobump/bio-gatk3-realignertargetcreator branch August 16, 2024 02:59
johanneskoester pushed a commit that referenced this pull request Aug 21, 2024
@github-actions
chore: release 4.1.0 (#3124)
51860ab 
🤖 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>
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