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fix: Removed unnecessary openjdk references #835

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merged 2 commits into from Nov 11, 2022

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fgvieira
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@fgvieira fgvieira commented Nov 9, 2022

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 enabled auto-merge (squash) November 9, 2022 14:01
@fgvieira fgvieira merged commit 0353285 into snakemake:master Nov 11, 2022
@fgvieira fgvieira deleted the fix_gatk_jdk branch November 12, 2022 17:56
johanneskoester pushed a commit that referenced this pull request Nov 23, 2022
🤖 I have created a release \*beep\* \*boop\*
---
###
[1.19.2](https://www.github.com/snakemake/snakemake-wrappers/compare/v1.19.1...v1.19.2)
(2022-11-18)


### Bug Fixes

* Removed unnecessary openjdk references
([#835](https://www.github.com/snakemake/snakemake-wrappers/issues/835))
([0353285](https://www.github.com/snakemake/snakemake-wrappers/commit/035328563254b7c5e1dc9ac0be8faedee066855e))


### Performance Improvements

* autobump bio/bismark/bismark
([#907](https://www.github.com/snakemake/snakemake-wrappers/issues/907))
([2c8dc87](https://www.github.com/snakemake/snakemake-wrappers/commit/2c8dc8769e5eac41d19a7b35fee7b41eadffca91))
* autobump bio/bwa-meme/mem
([#897](https://www.github.com/snakemake/snakemake-wrappers/issues/897))
([d377cce](https://www.github.com/snakemake/snakemake-wrappers/commit/d377cce4b70659d4b65bd083b5bb36f0cf212a8b))
* autobump bio/bwa-memx/mem
([#909](https://www.github.com/snakemake/snakemake-wrappers/issues/909))
([31974b1](https://www.github.com/snakemake/snakemake-wrappers/commit/31974b1a9dc8e60551c1a5f6e8e894602b067cf5))
* autobump bio/deeptools/computematrix
([#895](https://www.github.com/snakemake/snakemake-wrappers/issues/895))
([b0b1943](https://www.github.com/snakemake/snakemake-wrappers/commit/b0b1943bf1a6958972ec86829a7d6a32975c6d3e))
* autobump bio/deeptools/plotfingerprint
([#887](https://www.github.com/snakemake/snakemake-wrappers/issues/887))
([5157780](https://www.github.com/snakemake/snakemake-wrappers/commit/5157780b3e9baf0268ec75b13e3db4058fe9eac8))
* autobump bio/fastq_screen
([#916](https://www.github.com/snakemake/snakemake-wrappers/issues/916))
([6c62488](https://www.github.com/snakemake/snakemake-wrappers/commit/6c62488020b061dad87219e8b8d5034a58550e71))
* autobump bio/fgbio/groupreadsbyumi
([#908](https://www.github.com/snakemake/snakemake-wrappers/issues/908))
([caa4b85](https://www.github.com/snakemake/snakemake-wrappers/commit/caa4b854eebae9eb5faf0f09aac286a1b2a54595))
* autobump bio/gatk/depthofcoverage
([#905](https://www.github.com/snakemake/snakemake-wrappers/issues/905))
([8043b30](https://www.github.com/snakemake/snakemake-wrappers/commit/8043b30f7efdc41859c406c618b24c8842abcf08))
* autobump bio/gatk/mutect
([#892](https://www.github.com/snakemake/snakemake-wrappers/issues/892))
([6fcabfa](https://www.github.com/snakemake/snakemake-wrappers/commit/6fcabfa8990343810a6dd12c0ce0f0f9d4c70b5b))
* autobump bio/gatk/variantfiltration
([#911](https://www.github.com/snakemake/snakemake-wrappers/issues/911))
([b9cc5d4](https://www.github.com/snakemake/snakemake-wrappers/commit/b9cc5d47d1b6a558b639116fe8880aa3a1b659b2))
* autobump bio/homer/getDifferentialPeaks
([#894](https://www.github.com/snakemake/snakemake-wrappers/issues/894))
([fba57fa](https://www.github.com/snakemake/snakemake-wrappers/commit/fba57fa7b7dcfba2fcb32ae45994e3eb2b2fec64))
* autobump bio/homer/makeTagDirectory
([#899](https://www.github.com/snakemake/snakemake-wrappers/issues/899))
([762aa81](https://www.github.com/snakemake/snakemake-wrappers/commit/762aa81c64bce22ec907aa18ce40a2c1b42c7132))
* autobump bio/last/lastdb
([#889](https://www.github.com/snakemake/snakemake-wrappers/issues/889))
([f3ffc52](https://www.github.com/snakemake/snakemake-wrappers/commit/f3ffc52334d5c2f3d10e3d00eb887608e07f635b))
* autobump bio/meryl/count
([#896](https://www.github.com/snakemake/snakemake-wrappers/issues/896))
([c1dea53](https://www.github.com/snakemake/snakemake-wrappers/commit/c1dea53900835ac2c308025f0618cd59d89d33c9))
* autobump bio/paladin/prepare
([#900](https://www.github.com/snakemake/snakemake-wrappers/issues/900))
([f06905d](https://www.github.com/snakemake/snakemake-wrappers/commit/f06905daaa57e566218b6e76be67e5be06515ff3))
* autobump bio/pbmm2/index
([#893](https://www.github.com/snakemake/snakemake-wrappers/issues/893))
([7b84d5b](https://www.github.com/snakemake/snakemake-wrappers/commit/7b84d5b5d1dc88ca8dfd45f026ec3ef8ecc9d2c3))
* autobump bio/picard/mergesamfiles
([#906](https://www.github.com/snakemake/snakemake-wrappers/issues/906))
([c89123b](https://www.github.com/snakemake/snakemake-wrappers/commit/c89123b486fe9a6f91cb76d5b3ea1bf357c2e32e))
* autobump bio/pindel/pindel2vcf
([#904](https://www.github.com/snakemake/snakemake-wrappers/issues/904))
([7582c86](https://www.github.com/snakemake/snakemake-wrappers/commit/7582c86cb920b540a0a21f17fd68e27133c98c7b))
* autobump bio/qualimap/bamqc
([#912](https://www.github.com/snakemake/snakemake-wrappers/issues/912))
([d73c713](https://www.github.com/snakemake/snakemake-wrappers/commit/d73c7136937e3188a30c62c05b602886c75dad4b))
* autobump bio/qualimap/rnaseq
([#914](https://www.github.com/snakemake/snakemake-wrappers/issues/914))
([43ec0e7](https://www.github.com/snakemake/snakemake-wrappers/commit/43ec0e7ca5685f15a1d640d9c6f6bc927e770da7))
* autobump bio/rsem/calculate-expression
([#915](https://www.github.com/snakemake/snakemake-wrappers/issues/915))
([4a02028](https://www.github.com/snakemake/snakemake-wrappers/commit/4a020286194c579e63e229dde0f4427e398054be))
* autobump bio/salmon/index
([#917](https://www.github.com/snakemake/snakemake-wrappers/issues/917))
([9a7dd71](https://www.github.com/snakemake/snakemake-wrappers/commit/9a7dd71bf29c9c8810b388ae8cb93a54e6b84db7))
* autobump bio/salmon/quant
([#901](https://www.github.com/snakemake/snakemake-wrappers/issues/901))
([1abf483](https://www.github.com/snakemake/snakemake-wrappers/commit/1abf4835642646844227335d61883f791ed4c969))
* autobump bio/sambamba/index
([#903](https://www.github.com/snakemake/snakemake-wrappers/issues/903))
([e15388c](https://www.github.com/snakemake/snakemake-wrappers/commit/e15388c85668dee3b9a916ecf9c8e437764ffd3d))
* autobump bio/sambamba/slice
([#890](https://www.github.com/snakemake/snakemake-wrappers/issues/890))
([7d90b49](https://www.github.com/snakemake/snakemake-wrappers/commit/7d90b492656e1a9ff22a3f3b028bb23f822af693))
* autobump bio/seqtk/mergepe
([#910](https://www.github.com/snakemake/snakemake-wrappers/issues/910))
([374d337](https://www.github.com/snakemake/snakemake-wrappers/commit/374d337b784ebb82a33c07cbeacdd7c953a5c06a))
* autobump bio/snpsift/annotate
([#898](https://www.github.com/snakemake/snakemake-wrappers/issues/898))
([6aabee4](https://www.github.com/snakemake/snakemake-wrappers/commit/6aabee4cc1bca83c1435d1eae6d75de28003a84f))
* autobump bio/snpsift/varType
([#902](https://www.github.com/snakemake/snakemake-wrappers/issues/902))
([c200777](https://www.github.com/snakemake/snakemake-wrappers/commit/c20077773d39573920e67c2e3ff5fec57343f9c7))
* autobump bio/vep/plugins
([#913](https://www.github.com/snakemake/snakemake-wrappers/issues/913))
([298ab04](https://www.github.com/snakemake/snakemake-wrappers/commit/298ab04eb8cfa659917c0386b5df1c369fbcb695))
* autobump bio/vg/kmers
([#888](https://www.github.com/snakemake/snakemake-wrappers/issues/888))
([5570e67](https://www.github.com/snakemake/snakemake-wrappers/commit/5570e675fd639d1d28366b93832d562c6d9ec4e5))
* autobump bio/vg/sim
([#886](https://www.github.com/snakemake/snakemake-wrappers/issues/886))
([83c3189](https://www.github.com/snakemake/snakemake-wrappers/commit/83c3189322e414831ec37ce1ade2dfd0f5cf3bba))
* autobump utils/datavzrd
([#891](https://www.github.com/snakemake/snakemake-wrappers/issues/891))
([4a4e4ce](https://www.github.com/snakemake/snakemake-wrappers/commit/4a4e4ce81b2f51e91cc3fcab763d2f105645ae58))
---


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 pushed 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

<!-- Add a description of your PR here-->

### 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).
Phlya pushed a commit to Phlya/snakemake-wrappers that referenced this pull request Jan 10, 2023
🤖 I have created a release \*beep\* \*boop\*
---
###
[1.19.2](https://www.github.com/snakemake/snakemake-wrappers/compare/v1.19.1...v1.19.2)
(2022-11-18)


### Bug Fixes

* Removed unnecessary openjdk references
([snakemake#835](https://www.github.com/snakemake/snakemake-wrappers/issues/835))
([0353285](https://www.github.com/snakemake/snakemake-wrappers/commit/035328563254b7c5e1dc9ac0be8faedee066855e))


### Performance Improvements

* autobump bio/bismark/bismark
([snakemake#907](https://www.github.com/snakemake/snakemake-wrappers/issues/907))
([2c8dc87](https://www.github.com/snakemake/snakemake-wrappers/commit/2c8dc8769e5eac41d19a7b35fee7b41eadffca91))
* autobump bio/bwa-meme/mem
([snakemake#897](https://www.github.com/snakemake/snakemake-wrappers/issues/897))
([d377cce](https://www.github.com/snakemake/snakemake-wrappers/commit/d377cce4b70659d4b65bd083b5bb36f0cf212a8b))
* autobump bio/bwa-memx/mem
([snakemake#909](https://www.github.com/snakemake/snakemake-wrappers/issues/909))
([31974b1](https://www.github.com/snakemake/snakemake-wrappers/commit/31974b1a9dc8e60551c1a5f6e8e894602b067cf5))
* autobump bio/deeptools/computematrix
([snakemake#895](https://www.github.com/snakemake/snakemake-wrappers/issues/895))
([b0b1943](https://www.github.com/snakemake/snakemake-wrappers/commit/b0b1943bf1a6958972ec86829a7d6a32975c6d3e))
* autobump bio/deeptools/plotfingerprint
([snakemake#887](https://www.github.com/snakemake/snakemake-wrappers/issues/887))
([5157780](https://www.github.com/snakemake/snakemake-wrappers/commit/5157780b3e9baf0268ec75b13e3db4058fe9eac8))
* autobump bio/fastq_screen
([snakemake#916](https://www.github.com/snakemake/snakemake-wrappers/issues/916))
([6c62488](https://www.github.com/snakemake/snakemake-wrappers/commit/6c62488020b061dad87219e8b8d5034a58550e71))
* autobump bio/fgbio/groupreadsbyumi
([snakemake#908](https://www.github.com/snakemake/snakemake-wrappers/issues/908))
([caa4b85](https://www.github.com/snakemake/snakemake-wrappers/commit/caa4b854eebae9eb5faf0f09aac286a1b2a54595))
* autobump bio/gatk/depthofcoverage
([snakemake#905](https://www.github.com/snakemake/snakemake-wrappers/issues/905))
([8043b30](https://www.github.com/snakemake/snakemake-wrappers/commit/8043b30f7efdc41859c406c618b24c8842abcf08))
* autobump bio/gatk/mutect
([snakemake#892](https://www.github.com/snakemake/snakemake-wrappers/issues/892))
([6fcabfa](https://www.github.com/snakemake/snakemake-wrappers/commit/6fcabfa8990343810a6dd12c0ce0f0f9d4c70b5b))
* autobump bio/gatk/variantfiltration
([snakemake#911](https://www.github.com/snakemake/snakemake-wrappers/issues/911))
([b9cc5d4](https://www.github.com/snakemake/snakemake-wrappers/commit/b9cc5d47d1b6a558b639116fe8880aa3a1b659b2))
* autobump bio/homer/getDifferentialPeaks
([snakemake#894](https://www.github.com/snakemake/snakemake-wrappers/issues/894))
([fba57fa](https://www.github.com/snakemake/snakemake-wrappers/commit/fba57fa7b7dcfba2fcb32ae45994e3eb2b2fec64))
* autobump bio/homer/makeTagDirectory
([snakemake#899](https://www.github.com/snakemake/snakemake-wrappers/issues/899))
([762aa81](https://www.github.com/snakemake/snakemake-wrappers/commit/762aa81c64bce22ec907aa18ce40a2c1b42c7132))
* autobump bio/last/lastdb
([snakemake#889](https://www.github.com/snakemake/snakemake-wrappers/issues/889))
([f3ffc52](https://www.github.com/snakemake/snakemake-wrappers/commit/f3ffc52334d5c2f3d10e3d00eb887608e07f635b))
* autobump bio/meryl/count
([snakemake#896](https://www.github.com/snakemake/snakemake-wrappers/issues/896))
([c1dea53](https://www.github.com/snakemake/snakemake-wrappers/commit/c1dea53900835ac2c308025f0618cd59d89d33c9))
* autobump bio/paladin/prepare
([snakemake#900](https://www.github.com/snakemake/snakemake-wrappers/issues/900))
([f06905d](https://www.github.com/snakemake/snakemake-wrappers/commit/f06905daaa57e566218b6e76be67e5be06515ff3))
* autobump bio/pbmm2/index
([snakemake#893](https://www.github.com/snakemake/snakemake-wrappers/issues/893))
([7b84d5b](https://www.github.com/snakemake/snakemake-wrappers/commit/7b84d5b5d1dc88ca8dfd45f026ec3ef8ecc9d2c3))
* autobump bio/picard/mergesamfiles
([snakemake#906](https://www.github.com/snakemake/snakemake-wrappers/issues/906))
([c89123b](https://www.github.com/snakemake/snakemake-wrappers/commit/c89123b486fe9a6f91cb76d5b3ea1bf357c2e32e))
* autobump bio/pindel/pindel2vcf
([snakemake#904](https://www.github.com/snakemake/snakemake-wrappers/issues/904))
([7582c86](https://www.github.com/snakemake/snakemake-wrappers/commit/7582c86cb920b540a0a21f17fd68e27133c98c7b))
* autobump bio/qualimap/bamqc
([snakemake#912](https://www.github.com/snakemake/snakemake-wrappers/issues/912))
([d73c713](https://www.github.com/snakemake/snakemake-wrappers/commit/d73c7136937e3188a30c62c05b602886c75dad4b))
* autobump bio/qualimap/rnaseq
([snakemake#914](https://www.github.com/snakemake/snakemake-wrappers/issues/914))
([43ec0e7](https://www.github.com/snakemake/snakemake-wrappers/commit/43ec0e7ca5685f15a1d640d9c6f6bc927e770da7))
* autobump bio/rsem/calculate-expression
([snakemake#915](https://www.github.com/snakemake/snakemake-wrappers/issues/915))
([4a02028](https://www.github.com/snakemake/snakemake-wrappers/commit/4a020286194c579e63e229dde0f4427e398054be))
* autobump bio/salmon/index
([snakemake#917](https://www.github.com/snakemake/snakemake-wrappers/issues/917))
([9a7dd71](https://www.github.com/snakemake/snakemake-wrappers/commit/9a7dd71bf29c9c8810b388ae8cb93a54e6b84db7))
* autobump bio/salmon/quant
([snakemake#901](https://www.github.com/snakemake/snakemake-wrappers/issues/901))
([1abf483](https://www.github.com/snakemake/snakemake-wrappers/commit/1abf4835642646844227335d61883f791ed4c969))
* autobump bio/sambamba/index
([snakemake#903](https://www.github.com/snakemake/snakemake-wrappers/issues/903))
([e15388c](https://www.github.com/snakemake/snakemake-wrappers/commit/e15388c85668dee3b9a916ecf9c8e437764ffd3d))
* autobump bio/sambamba/slice
([snakemake#890](https://www.github.com/snakemake/snakemake-wrappers/issues/890))
([7d90b49](https://www.github.com/snakemake/snakemake-wrappers/commit/7d90b492656e1a9ff22a3f3b028bb23f822af693))
* autobump bio/seqtk/mergepe
([snakemake#910](https://www.github.com/snakemake/snakemake-wrappers/issues/910))
([374d337](https://www.github.com/snakemake/snakemake-wrappers/commit/374d337b784ebb82a33c07cbeacdd7c953a5c06a))
* autobump bio/snpsift/annotate
([snakemake#898](https://www.github.com/snakemake/snakemake-wrappers/issues/898))
([6aabee4](https://www.github.com/snakemake/snakemake-wrappers/commit/6aabee4cc1bca83c1435d1eae6d75de28003a84f))
* autobump bio/snpsift/varType
([snakemake#902](https://www.github.com/snakemake/snakemake-wrappers/issues/902))
([c200777](https://www.github.com/snakemake/snakemake-wrappers/commit/c20077773d39573920e67c2e3ff5fec57343f9c7))
* autobump bio/vep/plugins
([snakemake#913](https://www.github.com/snakemake/snakemake-wrappers/issues/913))
([298ab04](https://www.github.com/snakemake/snakemake-wrappers/commit/298ab04eb8cfa659917c0386b5df1c369fbcb695))
* autobump bio/vg/kmers
([snakemake#888](https://www.github.com/snakemake/snakemake-wrappers/issues/888))
([5570e67](https://www.github.com/snakemake/snakemake-wrappers/commit/5570e675fd639d1d28366b93832d562c6d9ec4e5))
* autobump bio/vg/sim
([snakemake#886](https://www.github.com/snakemake/snakemake-wrappers/issues/886))
([83c3189](https://www.github.com/snakemake/snakemake-wrappers/commit/83c3189322e414831ec37ce1ade2dfd0f5cf3bba))
* autobump utils/datavzrd
([snakemake#891](https://www.github.com/snakemake/snakemake-wrappers/issues/891))
([4a4e4ce](https://www.github.com/snakemake/snakemake-wrappers/commit/4a4e4ce81b2f51e91cc3fcab763d2f105645ae58))
---


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