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perf: Update Datavzrd to 2.36.3 #2696

Merged
merged 1 commit into from Feb 28, 2024
Merged

perf: Update Datavzrd to 2.36.3 #2696

merged 1 commit into from Feb 28, 2024

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fxwiegand
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QC

  • I confirm that:

For all wrappers added by this PR,

  • there is a test case which covers any introduced changes,
  • input: and output: file paths in the resulting rule can be changed arbitrarily,
  • either the wrapper can only use a single core, or the example rule contains a threads: x statement with x being a reasonable default,
  • rule names in the test case are in snake_case and somehow tell what the rule is about or match the tools purpose or name (e.g., map_reads for a step that maps reads),
  • all environment.yaml specifications follow the respective best practices,
  • the environment.yaml pinning has been updated by running snakedeploy pin-conda-envs environment.yaml on a linux machine,
  • wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in input: or output:),
  • all fields of the example rules in the Snakefiles and their entries are explained via comments (input:/output:/params: etc.),
  • stderr and/or stdout are logged correctly (log:), depending on the wrapped tool,
  • 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 (see here; this also means that using any Python tempfile default behavior works),
  • the meta.yaml contains a link to the documentation of the respective tool or command,
  • Snakefiles pass the linting (snakemake --lint),
  • Snakefiles are formatted with snakefmt,
  • Python wrapper scripts are formatted with black.
  • Conda environments use a minimal amount of channels, in recommended ordering. E.g. for bioconda, use (conda-forge, bioconda, nodefaults, as conda-forge should have highest priority and defaults channels are usually not needed because most packages are in conda-forge nowadays).

@FelixMoelder FelixMoelder merged commit baa8376 into master Feb 28, 2024
6 checks passed
@FelixMoelder FelixMoelder deleted the fxwiegand-patch-1 branch February 28, 2024 17:12
johanneskoester pushed a commit that referenced this pull request Mar 1, 2024
🤖 I have created a release \*beep\* \*boop\*
---
###
[3.4.1](https://www.github.com/snakemake/snakemake-wrappers/compare/v3.4.0...v3.4.1)
(2024-03-01)


### Performance Improvements

* autobump bio/gatk/applyvqsr
([#2705](https://www.github.com/snakemake/snakemake-wrappers/issues/2705))
([8c90ec7](https://www.github.com/snakemake/snakemake-wrappers/commit/8c90ec7dc40e1324bfaf419859362b58254f2184))
* autobump bio/gatk/baserecalibrator
([#2704](https://www.github.com/snakemake/snakemake-wrappers/issues/2704))
([0d6c664](https://www.github.com/snakemake/snakemake-wrappers/commit/0d6c664161dccc41e93fc2bf7d4aea424f54b2da))
* autobump bio/gatk/collectalleliccounts
([#2699](https://www.github.com/snakemake/snakemake-wrappers/issues/2699))
([9018e05](https://www.github.com/snakemake/snakemake-wrappers/commit/9018e0565890db75129c9a66dfaba712ae449d81))
* autobump bio/gatk/haplotypecaller
([#2698](https://www.github.com/snakemake/snakemake-wrappers/issues/2698))
([aa76a60](https://www.github.com/snakemake/snakemake-wrappers/commit/aa76a60ad436010bd578326454d5bb1652ddbbef))
* autobump bio/gatk/intervallisttobed
([#2700](https://www.github.com/snakemake/snakemake-wrappers/issues/2700))
([3d35d2b](https://www.github.com/snakemake/snakemake-wrappers/commit/3d35d2b6dc1d8f8144fadfe2b46b8af239f23f21))
* autobump bio/gatk/printreadsspark
([#2703](https://www.github.com/snakemake/snakemake-wrappers/issues/2703))
([a62781c](https://www.github.com/snakemake/snakemake-wrappers/commit/a62781c9ee05979fcb8c1790e06a75422ee7a12d))
* autobump bio/gatk/selectvariants
([#2707](https://www.github.com/snakemake/snakemake-wrappers/issues/2707))
([9815aa5](https://www.github.com/snakemake/snakemake-wrappers/commit/9815aa571a3704c0edc5e16cbfc349720c48a57e))
* autobump bio/gatk/variantstotable
([#2697](https://www.github.com/snakemake/snakemake-wrappers/issues/2697))
([0e6c7ef](https://www.github.com/snakemake/snakemake-wrappers/commit/0e6c7ef1248bc2a6a1324cf1dfc55a7e1015f9a3))
* autobump bio/gatk3/baserecalibrator
([#2702](https://www.github.com/snakemake/snakemake-wrappers/issues/2702))
([90a833a](https://www.github.com/snakemake/snakemake-wrappers/commit/90a833a2997d10bf160ecede87dca2ea390140ad))
* autobump bio/gatk3/indelrealigner
([#2701](https://www.github.com/snakemake/snakemake-wrappers/issues/2701))
([c13c656](https://www.github.com/snakemake/snakemake-wrappers/commit/c13c65623bd807769d66a55ca150ee1213eeb15d))
* autobump bio/gatk3/realignertargetcreator
([#2706](https://www.github.com/snakemake/snakemake-wrappers/issues/2706))
([4f3e20b](https://www.github.com/snakemake/snakemake-wrappers/commit/4f3e20b137ae19ed95f8e06c2f8e859a47485487))
* autobump bio/multiqc
([#2708](https://www.github.com/snakemake/snakemake-wrappers/issues/2708))
([4d60b0f](https://www.github.com/snakemake/snakemake-wrappers/commit/4d60b0fceee00697b088971cc264bc4ad2734855))
* autobump bio/open-cravat/module
([#2709](https://www.github.com/snakemake/snakemake-wrappers/issues/2709))
([c8ec2ae](https://www.github.com/snakemake/snakemake-wrappers/commit/c8ec2ae4f4b2633ca60d3a083ec2ab46a1f64f62))
* autobump bio/open-cravat/run
([#2710](https://www.github.com/snakemake/snakemake-wrappers/issues/2710))
([4268a26](https://www.github.com/snakemake/snakemake-wrappers/commit/4268a26087afc343cd6d5323c2e1eb1be89c78e7))
* autobump bio/picard/collectinsertsizemetrics
([#2711](https://www.github.com/snakemake/snakemake-wrappers/issues/2711))
([a2b2d66](https://www.github.com/snakemake/snakemake-wrappers/commit/a2b2d66b284c4a5a3a471f00f1dc0402c9b8a17c))
* autobump bio/vg/construct
([#2715](https://www.github.com/snakemake/snakemake-wrappers/issues/2715))
([7b1cde1](https://www.github.com/snakemake/snakemake-wrappers/commit/7b1cde1a0212e650a59147f0792a2df6dc363acd))
* autobump bio/vg/ids
([#2717](https://www.github.com/snakemake/snakemake-wrappers/issues/2717))
([e7b495b](https://www.github.com/snakemake/snakemake-wrappers/commit/e7b495bb3018959db51c5d5c534113be4bc0c055))
* autobump bio/vg/kmers
([#2716](https://www.github.com/snakemake/snakemake-wrappers/issues/2716))
([e5d6785](https://www.github.com/snakemake/snakemake-wrappers/commit/e5d67855029f10cb1831566ad8df9d028d131ee1))
* autobump bio/vg/merge
([#2713](https://www.github.com/snakemake/snakemake-wrappers/issues/2713))
([2609163](https://www.github.com/snakemake/snakemake-wrappers/commit/2609163931f94e960c584f0282002075dd61e23f))
* autobump bio/vg/prune
([#2714](https://www.github.com/snakemake/snakemake-wrappers/issues/2714))
([3abe763](https://www.github.com/snakemake/snakemake-wrappers/commit/3abe76370555309c2607d449c7f552f4465fd8ce))
* autobump bio/vg/sim
([#2712](https://www.github.com/snakemake/snakemake-wrappers/issues/2712))
([79dfbef](https://www.github.com/snakemake/snakemake-wrappers/commit/79dfbef6b6d9b902facf8547488b5095b70e0735))
* Update datavzrd to 2.36.2
([#2694](https://www.github.com/snakemake/snakemake-wrappers/issues/2694))
([b1ea355](https://www.github.com/snakemake/snakemake-wrappers/commit/b1ea355d3bd25db056e4a96b794769754dc61e3b))
* Update Datavzrd to 2.36.3
([#2696](https://www.github.com/snakemake/snakemake-wrappers/issues/2696))
([baa8376](https://www.github.com/snakemake/snakemake-wrappers/commit/baa8376bb89ea08a04323df7eed2e63766547180))
---


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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