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perf: Updated version of datavzrd to 2.19.1 #1328

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merged 1 commit into from May 4, 2023

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@manuelphilip manuelphilip commented May 4, 2023

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).

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LGTM

@dlaehnemann dlaehnemann merged commit fd89645 into snakemake:master May 4, 2023
7 checks passed
@manuelphilip manuelphilip deleted the patch-1 branch May 4, 2023 12:54
johanneskoester pushed a commit that referenced this pull request May 4, 2023
🤖 I have created a release \*beep\* \*boop\*
---
##
[1.29.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v1.28.0...v1.29.0)
(2023-05-04)


### Features

* Add seqkit subseq
([#1318](https://www.github.com/snakemake/snakemake-wrappers/issues/1318))
([262d9bb](https://www.github.com/snakemake/snakemake-wrappers/commit/262d9bb50cf8d03edca00916bc29fe5f1009209a))
* Deeptools Alignement seive
([#1320](https://www.github.com/snakemake/snakemake-wrappers/issues/1320))
([b7cb7ab](https://www.github.com/snakemake/snakemake-wrappers/commit/b7cb7ab5b70c1eec3b89d02f0bc94a2294e6a9aa))
* fix threads and new IO options in Bowtie2
([#1324](https://www.github.com/snakemake/snakemake-wrappers/issues/1324))
([a9c7117](https://www.github.com/snakemake/snakemake-wrappers/commit/a9c711718533f18429db50fb052549c49aa6fcf7))
* gatk CallCopyRatioSegments
([#1323](https://www.github.com/snakemake/snakemake-wrappers/issues/1323))
([528c91a](https://www.github.com/snakemake/snakemake-wrappers/commit/528c91a5b87ffe0d34964b01478a9b5d520ed80f))
* gatk collectalleliccount wrapper
([#1316](https://www.github.com/snakemake/snakemake-wrappers/issues/1316))
([158c328](https://www.github.com/snakemake/snakemake-wrappers/commit/158c328d1b846fb45c90c946edbcf2a7a0da15de))
* gatk collectreadcount wrapper
([#1315](https://www.github.com/snakemake/snakemake-wrappers/issues/1315))
([ee55de4](https://www.github.com/snakemake/snakemake-wrappers/commit/ee55de4cc2a850775ef94d5394f9a220844d8a7b))
* gatk DenoisedReadCounts wrapper
([#1319](https://www.github.com/snakemake/snakemake-wrappers/issues/1319))
([0288ace](https://www.github.com/snakemake/snakemake-wrappers/commit/0288ace7e61fbf2adf79514eefa2ff8f3566041e))
* gatk modelsegments wrapper
([#1321](https://www.github.com/snakemake/snakemake-wrappers/issues/1321))
([dfecc26](https://www.github.com/snakemake/snakemake-wrappers/commit/dfecc26de3c649c4661ac26203d846a54f7dd0b0))
* Pyroe make-spliced+unspliced
([#1290](https://www.github.com/snakemake/snakemake-wrappers/issues/1290))
([96a2cbb](https://www.github.com/snakemake/snakemake-wrappers/commit/96a2cbbf667fb45676087c2002fa875a76982e6b))


### Bug Fixes

* Lofreq indelqual
([#1325](https://www.github.com/snakemake/snakemake-wrappers/issues/1325))
([dabecf0](https://www.github.com/snakemake/snakemake-wrappers/commit/dabecf065975b7e53102221a63ec11b2c812cdee))


### Performance Improvements

* Updated version of datavzrd to 2.19.1
([#1328](https://www.github.com/snakemake/snakemake-wrappers/issues/1328))
([fd89645](https://www.github.com/snakemake/snakemake-wrappers/commit/fd89645aa28773f872a3b2f54192d66129852d83))
---


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>
tdayris pushed a commit to tdayris/snakemake-wrappers that referenced this pull request May 11, 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).
tdayris pushed a commit to tdayris/snakemake-wrappers that referenced this pull request May 11, 2023
🤖 I have created a release \*beep\* \*boop\*
---
##
[1.29.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v1.28.0...v1.29.0)
(2023-05-04)


### Features

* Add seqkit subseq
([snakemake#1318](https://www.github.com/snakemake/snakemake-wrappers/issues/1318))
([262d9bb](https://www.github.com/snakemake/snakemake-wrappers/commit/262d9bb50cf8d03edca00916bc29fe5f1009209a))
* Deeptools Alignement seive
([snakemake#1320](https://www.github.com/snakemake/snakemake-wrappers/issues/1320))
([b7cb7ab](https://www.github.com/snakemake/snakemake-wrappers/commit/b7cb7ab5b70c1eec3b89d02f0bc94a2294e6a9aa))
* fix threads and new IO options in Bowtie2
([snakemake#1324](https://www.github.com/snakemake/snakemake-wrappers/issues/1324))
([a9c7117](https://www.github.com/snakemake/snakemake-wrappers/commit/a9c711718533f18429db50fb052549c49aa6fcf7))
* gatk CallCopyRatioSegments
([snakemake#1323](https://www.github.com/snakemake/snakemake-wrappers/issues/1323))
([528c91a](https://www.github.com/snakemake/snakemake-wrappers/commit/528c91a5b87ffe0d34964b01478a9b5d520ed80f))
* gatk collectalleliccount wrapper
([snakemake#1316](https://www.github.com/snakemake/snakemake-wrappers/issues/1316))
([158c328](https://www.github.com/snakemake/snakemake-wrappers/commit/158c328d1b846fb45c90c946edbcf2a7a0da15de))
* gatk collectreadcount wrapper
([snakemake#1315](https://www.github.com/snakemake/snakemake-wrappers/issues/1315))
([ee55de4](https://www.github.com/snakemake/snakemake-wrappers/commit/ee55de4cc2a850775ef94d5394f9a220844d8a7b))
* gatk DenoisedReadCounts wrapper
([snakemake#1319](https://www.github.com/snakemake/snakemake-wrappers/issues/1319))
([0288ace](https://www.github.com/snakemake/snakemake-wrappers/commit/0288ace7e61fbf2adf79514eefa2ff8f3566041e))
* gatk modelsegments wrapper
([snakemake#1321](https://www.github.com/snakemake/snakemake-wrappers/issues/1321))
([dfecc26](https://www.github.com/snakemake/snakemake-wrappers/commit/dfecc26de3c649c4661ac26203d846a54f7dd0b0))
* Pyroe make-spliced+unspliced
([snakemake#1290](https://www.github.com/snakemake/snakemake-wrappers/issues/1290))
([96a2cbb](https://www.github.com/snakemake/snakemake-wrappers/commit/96a2cbbf667fb45676087c2002fa875a76982e6b))


### Bug Fixes

* Lofreq indelqual
([snakemake#1325](https://www.github.com/snakemake/snakemake-wrappers/issues/1325))
([dabecf0](https://www.github.com/snakemake/snakemake-wrappers/commit/dabecf065975b7e53102221a63ec11b2c812cdee))


### Performance Improvements

* Updated version of datavzrd to 2.19.1
([snakemake#1328](https://www.github.com/snakemake/snakemake-wrappers/issues/1328))
([fd89645](https://www.github.com/snakemake/snakemake-wrappers/commit/fd89645aa28773f872a3b2f54192d66129852d83))
---


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>
tdayris pushed a commit to tdayris/snakemake-wrappers that referenced this pull request Jul 5, 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).
tdayris pushed a commit to tdayris/snakemake-wrappers that referenced this pull request Jul 5, 2023
🤖 I have created a release \*beep\* \*boop\*
---
##
[1.29.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v1.28.0...v1.29.0)
(2023-05-04)


### Features

* Add seqkit subseq
([snakemake#1318](https://www.github.com/snakemake/snakemake-wrappers/issues/1318))
([262d9bb](https://www.github.com/snakemake/snakemake-wrappers/commit/262d9bb50cf8d03edca00916bc29fe5f1009209a))
* Deeptools Alignement seive
([snakemake#1320](https://www.github.com/snakemake/snakemake-wrappers/issues/1320))
([b7cb7ab](https://www.github.com/snakemake/snakemake-wrappers/commit/b7cb7ab5b70c1eec3b89d02f0bc94a2294e6a9aa))
* fix threads and new IO options in Bowtie2
([snakemake#1324](https://www.github.com/snakemake/snakemake-wrappers/issues/1324))
([a9c7117](https://www.github.com/snakemake/snakemake-wrappers/commit/a9c711718533f18429db50fb052549c49aa6fcf7))
* gatk CallCopyRatioSegments
([snakemake#1323](https://www.github.com/snakemake/snakemake-wrappers/issues/1323))
([528c91a](https://www.github.com/snakemake/snakemake-wrappers/commit/528c91a5b87ffe0d34964b01478a9b5d520ed80f))
* gatk collectalleliccount wrapper
([snakemake#1316](https://www.github.com/snakemake/snakemake-wrappers/issues/1316))
([158c328](https://www.github.com/snakemake/snakemake-wrappers/commit/158c328d1b846fb45c90c946edbcf2a7a0da15de))
* gatk collectreadcount wrapper
([snakemake#1315](https://www.github.com/snakemake/snakemake-wrappers/issues/1315))
([ee55de4](https://www.github.com/snakemake/snakemake-wrappers/commit/ee55de4cc2a850775ef94d5394f9a220844d8a7b))
* gatk DenoisedReadCounts wrapper
([snakemake#1319](https://www.github.com/snakemake/snakemake-wrappers/issues/1319))
([0288ace](https://www.github.com/snakemake/snakemake-wrappers/commit/0288ace7e61fbf2adf79514eefa2ff8f3566041e))
* gatk modelsegments wrapper
([snakemake#1321](https://www.github.com/snakemake/snakemake-wrappers/issues/1321))
([dfecc26](https://www.github.com/snakemake/snakemake-wrappers/commit/dfecc26de3c649c4661ac26203d846a54f7dd0b0))
* Pyroe make-spliced+unspliced
([snakemake#1290](https://www.github.com/snakemake/snakemake-wrappers/issues/1290))
([96a2cbb](https://www.github.com/snakemake/snakemake-wrappers/commit/96a2cbbf667fb45676087c2002fa875a76982e6b))


### Bug Fixes

* Lofreq indelqual
([snakemake#1325](https://www.github.com/snakemake/snakemake-wrappers/issues/1325))
([dabecf0](https://www.github.com/snakemake/snakemake-wrappers/commit/dabecf065975b7e53102221a63ec11b2c812cdee))


### Performance Improvements

* Updated version of datavzrd to 2.19.1
([snakemake#1328](https://www.github.com/snakemake/snakemake-wrappers/issues/1328))
([fd89645](https://www.github.com/snakemake/snakemake-wrappers/commit/fd89645aa28773f872a3b2f54192d66129852d83))
---


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