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perf: bump datavzrd to 2.23.2 #1729

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merged 1 commit into from Aug 10, 2023
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@manuelphilip manuelphilip commented Aug 10, 2023

Description

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,
  • 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 55a7066 into snakemake:master Aug 10, 2023
7 checks passed
johanneskoester pushed a commit that referenced this pull request Aug 21, 2023
🤖 I have created a release \*beep\* \*boop\*
---
##
[2.4.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v2.3.2...v2.4.0)
(2023-08-21)


### Features

* Add support for threads to GATK genomicsdbimport
([#1742](https://www.github.com/snakemake/snakemake-wrappers/issues/1742))
([b312e5c](https://www.github.com/snakemake/snakemake-wrappers/commit/b312e5c2fcd90ae709b5d799cdf378fb12a60301))
* add test for datavzrd
([#1755](https://www.github.com/snakemake/snakemake-wrappers/issues/1755))
([996bdcf](https://www.github.com/snakemake/snakemake-wrappers/commit/996bdcf2a96535b967dfa483c363a5496f4b3906))


### Performance Improvements

* autobump bio/bcftools/stats
([#1751](https://www.github.com/snakemake/snakemake-wrappers/issues/1751))
([56843f8](https://www.github.com/snakemake/snakemake-wrappers/commit/56843f87623f917a2820527d3b849a4e1263ca77))
* autobump bio/bismark/bismark2bedGraph
([#1747](https://www.github.com/snakemake/snakemake-wrappers/issues/1747))
([d954019](https://www.github.com/snakemake/snakemake-wrappers/commit/d954019a308672778c3d969e809a076c667ba88d))
* autobump bio/busco
([#1739](https://www.github.com/snakemake/snakemake-wrappers/issues/1739))
([d04d8d7](https://www.github.com/snakemake/snakemake-wrappers/commit/d04d8d73927354e8e43f222dc6d1d0de4dc1c4ce))
* autobump bio/delly
([#1735](https://www.github.com/snakemake/snakemake-wrappers/issues/1735))
([479ac84](https://www.github.com/snakemake/snakemake-wrappers/commit/479ac84e866f61b0d905e7c9e7048f2bdb0ec772))
* autobump bio/fastqc
([#1750](https://www.github.com/snakemake/snakemake-wrappers/issues/1750))
([8856ac6](https://www.github.com/snakemake/snakemake-wrappers/commit/8856ac647e5aea51f7aceab889cbc19fbf484311))
* autobump bio/gatk/estimatelibrarycomplexity
([#1736](https://www.github.com/snakemake/snakemake-wrappers/issues/1736))
([b318de6](https://www.github.com/snakemake/snakemake-wrappers/commit/b318de6011e7dbab95465bb3d8961668f7ec8a39))
* autobump bio/gatk3/printreads
([#1731](https://www.github.com/snakemake/snakemake-wrappers/issues/1731))
([b6fff95](https://www.github.com/snakemake/snakemake-wrappers/commit/b6fff95d6c25b3536d0999ed63b9e7aecc4bc586))
* autobump bio/mashmap
([#1737](https://www.github.com/snakemake/snakemake-wrappers/issues/1737))
([ae721ec](https://www.github.com/snakemake/snakemake-wrappers/commit/ae721ec4f0bbede932b54cb53046307506a7c659))
* autobump bio/picard/bedtointervallist
([#1734](https://www.github.com/snakemake/snakemake-wrappers/issues/1734))
([13e5cad](https://www.github.com/snakemake/snakemake-wrappers/commit/13e5cad53b86a84291b7420b37950cc111a7a7a2))
* autobump bio/qualimap/rnaseq
([#1746](https://www.github.com/snakemake/snakemake-wrappers/issues/1746))
([36835c5](https://www.github.com/snakemake/snakemake-wrappers/commit/36835c5cf60d488efd646fc7ff039bf7a9c7e8a9))
* autobump bio/samtools/depth
([#1738](https://www.github.com/snakemake/snakemake-wrappers/issues/1738))
([5d0f676](https://www.github.com/snakemake/snakemake-wrappers/commit/5d0f6761d8b2b11afeafe017d0566ae74fc0b0f9))
* autobump bio/snpsift/dbnsfp
([#1749](https://www.github.com/snakemake/snakemake-wrappers/issues/1749))
([cdfa888](https://www.github.com/snakemake/snakemake-wrappers/commit/cdfa8887ed1e3a196d9e1c7f58477212afc8d653))
* autobump bio/sra-tools/fasterq-dump
([#1732](https://www.github.com/snakemake/snakemake-wrappers/issues/1732))
([06e7b87](https://www.github.com/snakemake/snakemake-wrappers/commit/06e7b872c6de379a2c0452836b4f0c17e7f33fda))
* autobump bio/vg/kmers
([#1752](https://www.github.com/snakemake/snakemake-wrappers/issues/1752))
([cf84881](https://www.github.com/snakemake/snakemake-wrappers/commit/cf84881a288fb254ce0326f0864fad04c790d869))
* autobump bio/vg/merge
([#1748](https://www.github.com/snakemake/snakemake-wrappers/issues/1748))
([78f6716](https://www.github.com/snakemake/snakemake-wrappers/commit/78f671672ddeec3905d6a80751dc5d7cb7aa500f))
* autobump utils/cairosvg
([#1733](https://www.github.com/snakemake/snakemake-wrappers/issues/1733))
([3a48cd7](https://www.github.com/snakemake/snakemake-wrappers/commit/3a48cd719e6798b0b4041b929d8e6b7a92f83f0c))
* bump datavzrd to 2.23.2
([#1729](https://www.github.com/snakemake/snakemake-wrappers/issues/1729))
([55a7066](https://www.github.com/snakemake/snakemake-wrappers/commit/55a70669a000900cfd23c9bd4092f92b3eda208b))
* bump datavzrd to 2.23.3
([#1745](https://www.github.com/snakemake/snakemake-wrappers/issues/1745))
([dff136b](https://www.github.com/snakemake/snakemake-wrappers/commit/dff136b2da7a26e2368a96428885b12ec20c8d3b))
* bump datavzrd to 2.23.4
([#1753](https://www.github.com/snakemake/snakemake-wrappers/issues/1753))
([1b729e1](https://www.github.com/snakemake/snakemake-wrappers/commit/1b729e1f3ab0ab87725e12b484d993aa5627ede0))
---


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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