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feat: add galah wrapper #1754

Merged
merged 4 commits into from Aug 24, 2023
Merged

feat: add galah wrapper #1754

merged 4 commits into from Aug 24, 2023

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fgvieira
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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).

@fgvieira fgvieira marked this pull request as draft August 18, 2023 10:27
@fgvieira fgvieira marked this pull request as ready for review August 18, 2023 10:48
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@dlaehnemann dlaehnemann left a comment

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Nice and clean, just one very minor suggestion (which is a matter of style / taste, I guess). Thanks!

bio/galah/wrapper.py Outdated Show resolved Hide resolved
Co-authored-by: David Laehnemann <david.laehnemann@hhu.de>
@fgvieira fgvieira enabled auto-merge (squash) August 24, 2023 13:55
@fgvieira fgvieira merged commit 083688a into snakemake:master Aug 24, 2023
6 checks passed
johanneskoester pushed a commit that referenced this pull request Aug 25, 2023
🤖 I have created a release \*beep\* \*boop\*
---
##
[2.6.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v2.5.0...v2.6.0)
(2023-08-25)


### Features

* add galah wrapper
([#1754](https://www.github.com/snakemake/snakemake-wrappers/issues/1754))
([083688a](https://www.github.com/snakemake/snakemake-wrappers/commit/083688a059439b1b886ac2db95fd53530d5bef11))
* Enhanced-volcano
([#1521](https://www.github.com/snakemake/snakemake-wrappers/issues/1521))
([0bd316d](https://www.github.com/snakemake/snakemake-wrappers/commit/0bd316db902ed47d36250b4464f5d8710b295a61))
* Immunedeconv
([#1741](https://www.github.com/snakemake/snakemake-wrappers/issues/1741))
([97b5bde](https://www.github.com/snakemake/snakemake-wrappers/commit/97b5bdec2bcff9b26de7e6889cba72521b845e99))


### Bug Fixes

* Bwa mem threads
([#1743](https://www.github.com/snakemake/snakemake-wrappers/issues/1743))
([e35e312](https://www.github.com/snakemake/snakemake-wrappers/commit/e35e31219af8e7bf7b2f7174ddd7ade93abf7cad))


### Performance Improvements

* autobump bio/hifiasm
([#1768](https://www.github.com/snakemake/snakemake-wrappers/issues/1768))
([5795e2c](https://www.github.com/snakemake/snakemake-wrappers/commit/5795e2c31d0d6742908223fb7ff86fb186dd09f5))
* autobump bio/sourmash/compute
([#1767](https://www.github.com/snakemake/snakemake-wrappers/issues/1767))
([412f289](https://www.github.com/snakemake/snakemake-wrappers/commit/412f2892dc44c7218656b23dc6d83cb15e15eae0))
* autobump bio/vg/prune
([#1769](https://www.github.com/snakemake/snakemake-wrappers/issues/1769))
([fe30289](https://www.github.com/snakemake/snakemake-wrappers/commit/fe302896b2550585c257ac0311ed9c5ee462a2dd))
* update datavzrd 2.23.8
([#1764](https://www.github.com/snakemake/snakemake-wrappers/issues/1764))
([2f76671](https://www.github.com/snakemake/snakemake-wrappers/commit/2f766717bbf35dfaf748c02757b4f5eef0ff96ba))
---


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>
@fgvieira fgvieira deleted the galah branch August 25, 2023 09:25
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2 participants