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perf: Update Datavzrd #2735

Merged
merged 1 commit into from Mar 12, 2024
Merged

perf: Update Datavzrd #2735

merged 1 commit into from Mar 12, 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 41b562c into master Mar 12, 2024
6 checks passed
@FelixMoelder FelixMoelder deleted the fxwiegand-patch-1 branch March 12, 2024 08:10
johanneskoester pushed a commit that referenced this pull request Mar 13, 2024
🤖 I have created a release \*beep\* \*boop\*
---
##
[3.5.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v3.4.1...v3.5.0)
(2024-03-13)


### Features

* Genepred to bed
([#2726](https://www.github.com/snakemake/snakemake-wrappers/issues/2726))
([3998574](https://www.github.com/snakemake/snakemake-wrappers/commit/3998574d4c3cc02706ef4056dbb387835755e0f6))
* MultiQC automatically detects configuration from input file(s)
([#2722](https://www.github.com/snakemake/snakemake-wrappers/issues/2722))
([f61238d](https://www.github.com/snakemake/snakemake-wrappers/commit/f61238d350ba737aae0b2948857d7f50d5f124d7))
* Rseqc distribution
([#2737](https://www.github.com/snakemake/snakemake-wrappers/issues/2737))
([c732ff0](https://www.github.com/snakemake/snakemake-wrappers/commit/c732ff0c1fc5e139659a65c5b4495c67a1476985))
* Rseqc infer experiment
([#2730](https://www.github.com/snakemake/snakemake-wrappers/issues/2730))
([c597f2b](https://www.github.com/snakemake/snakemake-wrappers/commit/c597f2b50170ef0f3843624b38beb27f644022cc))
* Rseqc read duplication
([#2731](https://www.github.com/snakemake/snakemake-wrappers/issues/2731))
([2d5f9e7](https://www.github.com/snakemake/snakemake-wrappers/commit/2d5f9e79b6620cd2bc4627c643b0db846e4d576d))
* Rseqc read gc
([#2729](https://www.github.com/snakemake/snakemake-wrappers/issues/2729))
([739d809](https://www.github.com/snakemake/snakemake-wrappers/commit/739d809ad6d85a17bc5028a549d1e9e1b5262568))
* run Mutect2 multiple with input bam files
([#2736](https://www.github.com/snakemake/snakemake-wrappers/issues/2736))
([7b42689](https://www.github.com/snakemake/snakemake-wrappers/commit/7b426894a935eb071a842176e2449d481edf6d6c))


### Performance Improvements

* autobump bio/gseapy/gsea
([#2727](https://www.github.com/snakemake/snakemake-wrappers/issues/2727))
([400db30](https://www.github.com/snakemake/snakemake-wrappers/commit/400db30891d291605d7bb9e039937a62aea23107))
* autobump bio/sra-tools/fasterq-dump
([#2728](https://www.github.com/snakemake/snakemake-wrappers/issues/2728))
([92c9521](https://www.github.com/snakemake/snakemake-wrappers/commit/92c952124f885624e7725b672f8926cfb7386f76))
* Update Datavzrd
([#2735](https://www.github.com/snakemake/snakemake-wrappers/issues/2735))
([41b562c](https://www.github.com/snakemake/snakemake-wrappers/commit/41b562cf1c387294e7637e46cce66dd2bcb6218e))
* Update Datavzrd to 2.36.4
([#2720](https://www.github.com/snakemake/snakemake-wrappers/issues/2720))
([7611d30](https://www.github.com/snakemake/snakemake-wrappers/commit/7611d30950b85360cb91ff2b58895ae788e05c68))
* Update Datavzrd to 2.36.5
([#2733](https://www.github.com/snakemake/snakemake-wrappers/issues/2733))
([2fad8a1](https://www.github.com/snakemake/snakemake-wrappers/commit/2fad8a1bdf205033b799ce0048aae5af6c2b57c1))
* Update Datavzrd to 2.36.8
([#2738](https://www.github.com/snakemake/snakemake-wrappers/issues/2738))
([8c86447](https://www.github.com/snakemake/snakemake-wrappers/commit/8c86447fde4419e377e7a2c544a330343bbf19ab))
---


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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