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perf: Update Datavzrd to 2.36.10 #2915

Merged
merged 2 commits into from
May 2, 2024
Merged

perf: Update Datavzrd to 2.36.10 #2915

merged 2 commits into from
May 2, 2024

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fxwiegand
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@fxwiegand fxwiegand commented May 2, 2024

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).

@johanneskoester johanneskoester merged commit c0a7ddf into master May 2, 2024
6 checks passed
@johanneskoester johanneskoester deleted the fxwiegand-patch-1 branch May 2, 2024 19:45
johanneskoester pushed a commit that referenced this pull request May 2, 2024
🤖 I have created a release \*beep\* \*boop\*
---
##
[3.10.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v3.9.0...v3.10.0)
(2024-05-02)


### Features

* Add wrapper for filtering TTree in ROOT
([#2900](https://www.github.com/snakemake/snakemake-wrappers/issues/2900))
([c294552](https://www.github.com/snakemake/snakemake-wrappers/commit/c294552aa6b19b2cbdda4c650af47f1b83733b32))
* enable YTE templating in datavzrd config file
([#2916](https://www.github.com/snakemake/snakemake-wrappers/issues/2916))
([97262a5](https://www.github.com/snakemake/snakemake-wrappers/commit/97262a50efe2293b473f02b6761c4f95e0aa35a3))


### Performance Improvements

* autobump bio/cooltools/dots
([#2908](https://www.github.com/snakemake/snakemake-wrappers/issues/2908))
([7f53f54](https://www.github.com/snakemake/snakemake-wrappers/commit/7f53f54a96802e6ef1a401bbb5b4c25bc9611491))
* autobump bio/cooltools/eigs_cis
([#2904](https://www.github.com/snakemake/snakemake-wrappers/issues/2904))
([efe1887](https://www.github.com/snakemake/snakemake-wrappers/commit/efe18871eea04b55f8c921fb0ff19ef896c0dfb2))
* autobump bio/cooltools/eigs_trans
([#2903](https://www.github.com/snakemake/snakemake-wrappers/issues/2903))
([843e331](https://www.github.com/snakemake/snakemake-wrappers/commit/843e331b929bcf72d7be161c457f8541a6cd66d2))
* autobump bio/cooltools/expected_cis
([#2902](https://www.github.com/snakemake/snakemake-wrappers/issues/2902))
([c9ef619](https://www.github.com/snakemake/snakemake-wrappers/commit/c9ef619b858f59d4532e0df16fd9a6909019ea7c))
* autobump bio/cooltools/expected_trans
([#2909](https://www.github.com/snakemake/snakemake-wrappers/issues/2909))
([91d92d1](https://www.github.com/snakemake/snakemake-wrappers/commit/91d92d1b9dc0016fecf1dbd03615de116e388cc1))
* autobump bio/cooltools/insulation
([#2906](https://www.github.com/snakemake/snakemake-wrappers/issues/2906))
([f51323a](https://www.github.com/snakemake/snakemake-wrappers/commit/f51323afd11f6a3310862cee1542fb6776272f98))
* autobump bio/cooltools/pileup
([#2905](https://www.github.com/snakemake/snakemake-wrappers/issues/2905))
([6aa0897](https://www.github.com/snakemake/snakemake-wrappers/commit/6aa089798d3e8e4b80ce96d8e1f3ccc349c20b46))
* autobump bio/cooltools/saddle
([#2907](https://www.github.com/snakemake/snakemake-wrappers/issues/2907))
([925f413](https://www.github.com/snakemake/snakemake-wrappers/commit/925f413403ba2d970f003cd8d6ddfdbf29d6c624))
* autobump bio/gatk/applybqsrspark
([#2911](https://www.github.com/snakemake/snakemake-wrappers/issues/2911))
([cbe905b](https://www.github.com/snakemake/snakemake-wrappers/commit/cbe905b271568c52bbaa687ee101d15b29ef4164))
* autobump bio/gatk3/indelrealigner
([#2910](https://www.github.com/snakemake/snakemake-wrappers/issues/2910))
([40aa8f1](https://www.github.com/snakemake/snakemake-wrappers/commit/40aa8f1794a46b9285cf88d93451be88d83c67e6))
* autobump bio/mapdamage2
([#2912](https://www.github.com/snakemake/snakemake-wrappers/issues/2912))
([ea1bfbd](https://www.github.com/snakemake/snakemake-wrappers/commit/ea1bfbd33ba026022a7364903aaa42983b03f3ab))
* autobump bio/open-cravat/module
([#2913](https://www.github.com/snakemake/snakemake-wrappers/issues/2913))
([593839d](https://www.github.com/snakemake/snakemake-wrappers/commit/593839d30d39f9c08721ac373d22721a8017b66a))
* autobump bio/open-cravat/run
([#2914](https://www.github.com/snakemake/snakemake-wrappers/issues/2914))
([476823b](https://www.github.com/snakemake/snakemake-wrappers/commit/476823bfb83184116639be0a62bc47540255f6b3))
* Update Datavzrd to 2.36.10
([#2915](https://www.github.com/snakemake/snakemake-wrappers/issues/2915))
([c0a7ddf](https://www.github.com/snakemake/snakemake-wrappers/commit/c0a7ddff4bd0cc827e7c143e7e0dbf5f13f2e148))
---


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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