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fix: channel definitions for cooltools (and update version to 0.5.2), genefuse, genomescope, qualimap and meryl #980

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merged 2 commits into from Jan 20, 2023

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johanneskoester
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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).

@Phlya
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Phlya commented Jan 20, 2023

I think this PR for the cooltools recipe should fix the tests here: bioconda/bioconda-recipes#38928

@johanneskoester johanneskoester merged commit 26271ac into master Jan 20, 2023
@johanneskoester johanneskoester deleted the fix/channel-definitions branch January 20, 2023 15:58
johanneskoester pushed a commit that referenced this pull request Jan 20, 2023
🤖 I have created a release \*beep\* \*boop\*
---
###
[1.21.4](https://www.github.com/snakemake/snakemake-wrappers/compare/v1.21.3...v1.21.4)
(2023-01-20)


### Bug Fixes

* channel definitions for cooltools (and update version to 0.5.2),
genefuse, genomescope, qualimap and meryl
([#980](https://www.github.com/snakemake/snakemake-wrappers/issues/980))
([26271ac](https://www.github.com/snakemake/snakemake-wrappers/commit/26271acfb27c02d51d2a8cc0922b4780998e6b53))
* RSEM-calculate-expression wrapper with FASTQ-files as input +
Integration of test case
([#970](https://www.github.com/snakemake/snakemake-wrappers/issues/970))
([ea9c897](https://www.github.com/snakemake/snakemake-wrappers/commit/ea9c8978259c87156f4e48711eed0172a8966209))
---


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