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feat: add wrapper for coolpuppy #554

Merged
merged 51 commits into from Nov 2, 2022
Merged

feat: add wrapper for coolpuppy #554

merged 51 commits into from Nov 2, 2022

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Phlya
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@Phlya Phlya commented Sep 15, 2022

Description

Created a wrapper for coolpup.py (https://github.com/open2c/coolpuppy)

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 Phlya changed the title featr: add wrapper for coolpuppy feat: add wrapper for coolpuppy Sep 15, 2022
@Phlya Phlya marked this pull request as ready for review November 2, 2022 09:52
bio/coolpuppy/wrapper.py Outdated Show resolved Hide resolved
@Phlya
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Phlya commented Nov 2, 2022

@fgvieira thank you for approving! I just noticed that because I run black on everything I changed formatting for a lot of the other tests, so I reverted those changes now, and also reran black on the file you changed.

@fgvieira fgvieira merged commit 60f1fc1 into snakemake:master Nov 2, 2022
@Phlya
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Phlya commented Nov 2, 2022

Thanks a lot @fgvieira !

johanneskoester pushed a commit that referenced this pull request Nov 8, 2022
🤖 I have created a release \*beep\* \*boop\*
---
##
[1.19.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v1.18.3...v1.19.0)
(2022-11-08)


### Features

* add wrapper for coolpuppy
([#554](https://www.github.com/snakemake/snakemake-wrappers/issues/554))
([60f1fc1](https://www.github.com/snakemake/snakemake-wrappers/commit/60f1fc1a895fff794569fefa51312199a7e0bfd2))


### Bug Fixes

* fixed GATK3 conda channel priorities and code reformat
([#534](https://www.github.com/snakemake/snakemake-wrappers/issues/534))
([43e5a16](https://www.github.com/snakemake/snakemake-wrappers/commit/43e5a16c1bb88ea09999278d12eaee89c8d4e424))


### Performance Improvements

* autobump bio/bismark/deduplicate_bismark
([#672](https://www.github.com/snakemake/snakemake-wrappers/issues/672))
([c4ee12f](https://www.github.com/snakemake/snakemake-wrappers/commit/c4ee12f83c544833aa4f807b60e691516c030bf3))
* autobump bio/gatk/variantrecalibrator
([#773](https://www.github.com/snakemake/snakemake-wrappers/issues/773))
([8de1652](https://www.github.com/snakemake/snakemake-wrappers/commit/8de1652264379da3e83e4cc0b6fb01d40699de69))
* autobump bio/hmmer/hmmscan
([#830](https://www.github.com/snakemake/snakemake-wrappers/issues/830))
([727b385](https://www.github.com/snakemake/snakemake-wrappers/commit/727b385701a695a0a352275a0e3dcd1d19707056))
* autobump bio/picard/bedtointervallist
([#833](https://www.github.com/snakemake/snakemake-wrappers/issues/833))
([f1faa62](https://www.github.com/snakemake/snakemake-wrappers/commit/f1faa6244fde6ff28f26169aaae0f04c17723910))
* autobump bio/picard/collectalignmentsummarymetrics
([#831](https://www.github.com/snakemake/snakemake-wrappers/issues/831))
([c264c15](https://www.github.com/snakemake/snakemake-wrappers/commit/c264c15a32439c40029938ed2dce285e4e2bf9e3))
* autobump bio/picard/collectinsertsizemetrics
([#834](https://www.github.com/snakemake/snakemake-wrappers/issues/834))
([8381cd8](https://www.github.com/snakemake/snakemake-wrappers/commit/8381cd8ab874d09a3d9295c846a2c8c7cb3c93bd))
* autobump bio/seqtk/seq
([#832](https://www.github.com/snakemake/snakemake-wrappers/issues/832))
([754c4df](https://www.github.com/snakemake/snakemake-wrappers/commit/754c4dfda12338f04610377a70a87ca1b51f3939))
* update datavzrd wrapper to version 2.7.2
([12e47fd](https://www.github.com/snakemake/snakemake-wrappers/commit/12e47fdc05b2c603e9970a7a2ed9fe70e226249e))
---


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>
Phlya added a commit to Phlya/snakemake-wrappers that referenced this pull request Jan 10, 2023
<!-- Ensure that the PR title follows conventional commit style (<type>:
<description>)-->
<!-- Possible types are here:
https://github.com/commitizen/conventional-commit-types/blob/master/index.json
-->

### Description

Created a wrapper for coolpup.py (https://github.com/open2c/coolpuppy)

### QC
<!-- Make sure that you can tick the boxes below. -->

* [x] 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](https://en.wikipedia.org/wiki/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](https://stackoverflow.com/a/64594513/2352071),
* 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 `Snakefile`s 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](https://docs.python.org/3/library/tempfile.html#tempfile.gettempdir);
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,
* `Snakefile`s pass the linting (`snakemake --lint`),
* `Snakefile`s are formatted with
[snakefmt](https://github.com/snakemake/snakefmt),
* Python wrapper scripts are formatted with
[black](https://black.readthedocs.io).
* 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).

Co-authored-by: Filipe G. Vieira <fgarrettvieira@gmail.com>
Phlya pushed a commit to Phlya/snakemake-wrappers that referenced this pull request Jan 10, 2023
🤖 I have created a release \*beep\* \*boop\*
---
##
[1.19.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v1.18.3...v1.19.0)
(2022-11-08)


### Features

* add wrapper for coolpuppy
([snakemake#554](https://www.github.com/snakemake/snakemake-wrappers/issues/554))
([60f1fc1](https://www.github.com/snakemake/snakemake-wrappers/commit/60f1fc1a895fff794569fefa51312199a7e0bfd2))


### Bug Fixes

* fixed GATK3 conda channel priorities and code reformat
([snakemake#534](https://www.github.com/snakemake/snakemake-wrappers/issues/534))
([43e5a16](https://www.github.com/snakemake/snakemake-wrappers/commit/43e5a16c1bb88ea09999278d12eaee89c8d4e424))


### Performance Improvements

* autobump bio/bismark/deduplicate_bismark
([snakemake#672](https://www.github.com/snakemake/snakemake-wrappers/issues/672))
([c4ee12f](https://www.github.com/snakemake/snakemake-wrappers/commit/c4ee12f83c544833aa4f807b60e691516c030bf3))
* autobump bio/gatk/variantrecalibrator
([snakemake#773](https://www.github.com/snakemake/snakemake-wrappers/issues/773))
([8de1652](https://www.github.com/snakemake/snakemake-wrappers/commit/8de1652264379da3e83e4cc0b6fb01d40699de69))
* autobump bio/hmmer/hmmscan
([snakemake#830](https://www.github.com/snakemake/snakemake-wrappers/issues/830))
([727b385](https://www.github.com/snakemake/snakemake-wrappers/commit/727b385701a695a0a352275a0e3dcd1d19707056))
* autobump bio/picard/bedtointervallist
([snakemake#833](https://www.github.com/snakemake/snakemake-wrappers/issues/833))
([f1faa62](https://www.github.com/snakemake/snakemake-wrappers/commit/f1faa6244fde6ff28f26169aaae0f04c17723910))
* autobump bio/picard/collectalignmentsummarymetrics
([snakemake#831](https://www.github.com/snakemake/snakemake-wrappers/issues/831))
([c264c15](https://www.github.com/snakemake/snakemake-wrappers/commit/c264c15a32439c40029938ed2dce285e4e2bf9e3))
* autobump bio/picard/collectinsertsizemetrics
([snakemake#834](https://www.github.com/snakemake/snakemake-wrappers/issues/834))
([8381cd8](https://www.github.com/snakemake/snakemake-wrappers/commit/8381cd8ab874d09a3d9295c846a2c8c7cb3c93bd))
* autobump bio/seqtk/seq
([snakemake#832](https://www.github.com/snakemake/snakemake-wrappers/issues/832))
([754c4df](https://www.github.com/snakemake/snakemake-wrappers/commit/754c4dfda12338f04610377a70a87ca1b51f3939))
* update datavzrd wrapper to version 2.7.2
([12e47fd](https://www.github.com/snakemake/snakemake-wrappers/commit/12e47fdc05b2c603e9970a7a2ed9fe70e226249e))
---


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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