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perf: update picard markduplicates #1761

Merged
merged 1 commit into from Aug 23, 2023
Merged

perf: update picard markduplicates #1761

merged 1 commit into from Aug 23, 2023

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FelixMoelder
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Description

Update snakemake-wrapper-utils as it fixes a bug where mem_mb is ignored.

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).

@fgvieira fgvieira merged commit 0c8aad0 into master Aug 23, 2023
6 checks passed
@fgvieira fgvieira deleted the update_picard branch August 23, 2023 08:32
johanneskoester pushed a commit that referenced this pull request Aug 24, 2023
🤖 I have created a release \*beep\* \*boop\*
---
##
[2.5.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v2.4.0...v2.5.0)
(2023-08-24)


### Features

* bedtools split wrapper
([#1744](https://www.github.com/snakemake/snakemake-wrappers/issues/1744))
([bad454d](https://www.github.com/snakemake/snakemake-wrappers/commit/bad454d662d15c8beac15ffa2307164d4d708d07))


### Bug Fixes

* ensembl-variation - remove index
([#1760](https://www.github.com/snakemake/snakemake-wrappers/issues/1760))
([702a85b](https://www.github.com/snakemake/snakemake-wrappers/commit/702a85b7a2564fc9e94038825a12ed514192bc78))


### Performance Improvements

* bump datavzrd to 2.23.6
([#1757](https://www.github.com/snakemake/snakemake-wrappers/issues/1757))
([c500eb9](https://www.github.com/snakemake/snakemake-wrappers/commit/c500eb9682ef1230a1023211b1d96443cb341ab7))
* update datavzrd 2.23.7
([#1763](https://www.github.com/snakemake/snakemake-wrappers/issues/1763))
([b19813d](https://www.github.com/snakemake/snakemake-wrappers/commit/b19813d62a43db1d168087dccb62f85cd466a4cf))
* update picard markduplicates
([#1761](https://www.github.com/snakemake/snakemake-wrappers/issues/1761))
([0c8aad0](https://www.github.com/snakemake/snakemake-wrappers/commit/0c8aad0a9e786850d49c49bb0baef21b5335883d))
* update snakemake wrapper utils
([#1762](https://www.github.com/snakemake/snakemake-wrappers/issues/1762))
([371f337](https://www.github.com/snakemake/snakemake-wrappers/commit/371f3376d27efcacb679e0b2b645ba6ee33be24c))
* update vep annotate
([#1759](https://www.github.com/snakemake/snakemake-wrappers/issues/1759))
([f7e372f](https://www.github.com/snakemake/snakemake-wrappers/commit/f7e372f4d1576306975ad611e5aeb1c335b6658a))
---


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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2 participants