Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

perf: update datavzrd wrapper to 2.12.0 #973

Merged
merged 1 commit into from Jan 10, 2023

Conversation

johanneskoester
Copy link
Contributor

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).

@johanneskoester johanneskoester merged commit 8523e73 into master Jan 10, 2023
@johanneskoester johanneskoester deleted the bump/datavzrd-2.12.0 branch January 10, 2023 15:39
johanneskoester pushed a commit that referenced this pull request Jan 10, 2023
🤖 I have created a release \*beep\* \*boop\*
---
###
[1.21.2](https://www.github.com/snakemake/snakemake-wrappers/compare/v1.21.1...v1.21.2)
(2023-01-10)


### Bug Fixes

* make 'params: extra=' optional for rbt collapse_reads_to_fragments-bam
wrapper
([#968](https://www.github.com/snakemake/snakemake-wrappers/issues/968))
([03463da](https://www.github.com/snakemake/snakemake-wrappers/commit/03463da5ea60046d7c9a1a33459d3296c3ddb98c))


### Performance Improvements

* update datavzrd wrapper to 2.12.0
([#973](https://www.github.com/snakemake/snakemake-wrappers/issues/973))
([8523e73](https://www.github.com/snakemake/snakemake-wrappers/commit/8523e737ca0a5d7ae28a8a98b0988d6ea9e7f67b))
---


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>
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

None yet

1 participant