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feat: update arriba and star_arriba meta-wrapper #963

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merged 19 commits into from Dec 12, 2022
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@FelixMoelder FelixMoelder commented Dec 9, 2022

Description

This update arriba to version 2.3 and also the meta-wrapper as there where some changes of the command line parameters.
Also the meta wrapper was using a absolut path while the referenced file is defined in the input. So this is now called implicitly.

In addition I would like to discuss if the Test-Snakefile should be more generic.
The arriba-rule currently definies a blacklist-file as parameter while it is not part of the input.
In addition the contigs are also limited to chromosome 1 and 2.
As I would expect that a meta wrapper should work out of the box with default parameters when imported as a module it appears reasonable to me to remove this parameters (if this does not make the CI run forever).

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).

@FelixMoelder FelixMoelder changed the title feat: update arriba feat: update arriba and star_arriba meta-wrapper Dec 9, 2022
@johanneskoester johanneskoester merged commit f75d997 into master Dec 12, 2022
@johanneskoester johanneskoester deleted the update_arriba branch December 12, 2022 15:00
johanneskoester pushed a commit that referenced this pull request Dec 12, 2022
🤖 I have created a release \*beep\* \*boop\*
---
##
[1.21.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v1.20.0...v1.21.0)
(2022-12-12)


### Features

* tmpdir in Sambamba wrappers
([#960](https://www.github.com/snakemake/snakemake-wrappers/issues/960))
([a8333a3](https://www.github.com/snakemake/snakemake-wrappers/commit/a8333a3e44d3eac30453860f1793678d01167e40))
* update arriba and star_arriba meta-wrapper
([#963](https://www.github.com/snakemake/snakemake-wrappers/issues/963))
([f75d997](https://www.github.com/snakemake/snakemake-wrappers/commit/f75d997ca582e20165adbb34e55ce2224136081d))


### Bug Fixes

* updated parsing of bcftools opts
([#959](https://www.github.com/snakemake/snakemake-wrappers/issues/959))
([0af69c9](https://www.github.com/snakemake/snakemake-wrappers/commit/0af69c9f5ea2e016ea70ebe8a44747dc6fbd3e30))


### Performance Improvements

* autobump bio/bwa-memx/index
([#955](https://www.github.com/snakemake/snakemake-wrappers/issues/955))
([f51c0d6](https://www.github.com/snakemake/snakemake-wrappers/commit/f51c0d6e1cc6dfe714a0ef875bd68c0401dcc21a))
* autobump bio/cooltools/pileup
([#948](https://www.github.com/snakemake/snakemake-wrappers/issues/948))
([bf28d88](https://www.github.com/snakemake/snakemake-wrappers/commit/bf28d88b33aff888d9b3dc339b8a740a7e2017c8))
* autobump bio/dada2/assign-taxonomy
([#946](https://www.github.com/snakemake/snakemake-wrappers/issues/946))
([ed9ebfb](https://www.github.com/snakemake/snakemake-wrappers/commit/ed9ebfb588af703fe550cf71945ee5b684efa0d8))
* autobump bio/diamond/makedb
([#944](https://www.github.com/snakemake/snakemake-wrappers/issues/944))
([a95b5db](https://www.github.com/snakemake/snakemake-wrappers/commit/a95b5db5d7c722804b9e4ecb3fa375a76e4f3191))
* autobump bio/gatk/genotypegvcfs
([#951](https://www.github.com/snakemake/snakemake-wrappers/issues/951))
([5fb96d8](https://www.github.com/snakemake/snakemake-wrappers/commit/5fb96d8e8e43b3350ba2833f291c09d3e7ea1ff0))
* autobump bio/gatk/selectvariants
([#947](https://www.github.com/snakemake/snakemake-wrappers/issues/947))
([5f697b8](https://www.github.com/snakemake/snakemake-wrappers/commit/5f697b80cf3acee5367efd2fddc58aa7828abba9))
* autobump bio/homer/annotatePeaks
([#952](https://www.github.com/snakemake/snakemake-wrappers/issues/952))
([8f1270d](https://www.github.com/snakemake/snakemake-wrappers/commit/8f1270de93dd613e1d3f4042ed5c2c3c099b87b5))
* autobump bio/homer/mergePeaks
([#957](https://www.github.com/snakemake/snakemake-wrappers/issues/957))
([0330a43](https://www.github.com/snakemake/snakemake-wrappers/commit/0330a434160a5a015c19fb76a9c67665ace630ff))
* autobump bio/jellyfish/count
([#950](https://www.github.com/snakemake/snakemake-wrappers/issues/950))
([0a6f68d](https://www.github.com/snakemake/snakemake-wrappers/commit/0a6f68db8723f2c3f8a794d33badef8e4e32a773))
* autobump bio/last/lastal
([#942](https://www.github.com/snakemake/snakemake-wrappers/issues/942))
([8e5ef69](https://www.github.com/snakemake/snakemake-wrappers/commit/8e5ef69bc49fc2b911b7b9da6ba8f97c6149590b))
* autobump bio/microphaser/build_reference
([#943](https://www.github.com/snakemake/snakemake-wrappers/issues/943))
([1e7ece5](https://www.github.com/snakemake/snakemake-wrappers/commit/1e7ece5157bab0a83608a14cbdf45bced50322f0))
* autobump bio/picard/collecttargetedpcrmetrics
([#949](https://www.github.com/snakemake/snakemake-wrappers/issues/949))
([5239da9](https://www.github.com/snakemake/snakemake-wrappers/commit/5239da9b112d0ad5af6e0f79275b162d9a2b3f57))
* autobump bio/transdecoder/longorfs
([#956](https://www.github.com/snakemake/snakemake-wrappers/issues/956))
([54c2b74](https://www.github.com/snakemake/snakemake-wrappers/commit/54c2b74e6913cef43fa81a0fd86e997d12c37cde))
* autobump bio/tximport
([#954](https://www.github.com/snakemake/snakemake-wrappers/issues/954))
([4942f36](https://www.github.com/snakemake/snakemake-wrappers/commit/4942f365b97cabeb7478113aece432d2439ac9ce))
* autobump bio/varscan/somatic
([#958](https://www.github.com/snakemake/snakemake-wrappers/issues/958))
([28df43c](https://www.github.com/snakemake/snakemake-wrappers/commit/28df43c261751477a9cc888c30794709795e9dcb))
---


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

This update arriba to version 2.3 and also the meta-wrapper as there
where some changes of the command line parameters.
Also the meta wrapper was using a absolut path while the referenced file
is defined in the input. So this is now called implicitly.

In addition I would like to discuss if the Test-Snakefile should be more
generic.
The arriba-rule currently definies a blacklist-file as parameter while
it is not part of the input.
In addition the contigs are also limited to chromosome 1 and 2.
As I would expect that a meta wrapper should work out of the box with
default parameters when imported as a module it appears reasonable to me
to remove this parameters (if this does not make the CI run forever).
### 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\*
---
##
[1.21.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v1.20.0...v1.21.0)
(2022-12-12)


### Features

* tmpdir in Sambamba wrappers
([snakemake#960](https://www.github.com/snakemake/snakemake-wrappers/issues/960))
([a8333a3](https://www.github.com/snakemake/snakemake-wrappers/commit/a8333a3e44d3eac30453860f1793678d01167e40))
* update arriba and star_arriba meta-wrapper
([snakemake#963](https://www.github.com/snakemake/snakemake-wrappers/issues/963))
([f75d997](https://www.github.com/snakemake/snakemake-wrappers/commit/f75d997ca582e20165adbb34e55ce2224136081d))


### Bug Fixes

* updated parsing of bcftools opts
([snakemake#959](https://www.github.com/snakemake/snakemake-wrappers/issues/959))
([0af69c9](https://www.github.com/snakemake/snakemake-wrappers/commit/0af69c9f5ea2e016ea70ebe8a44747dc6fbd3e30))


### Performance Improvements

* autobump bio/bwa-memx/index
([snakemake#955](https://www.github.com/snakemake/snakemake-wrappers/issues/955))
([f51c0d6](https://www.github.com/snakemake/snakemake-wrappers/commit/f51c0d6e1cc6dfe714a0ef875bd68c0401dcc21a))
* autobump bio/cooltools/pileup
([snakemake#948](https://www.github.com/snakemake/snakemake-wrappers/issues/948))
([bf28d88](https://www.github.com/snakemake/snakemake-wrappers/commit/bf28d88b33aff888d9b3dc339b8a740a7e2017c8))
* autobump bio/dada2/assign-taxonomy
([snakemake#946](https://www.github.com/snakemake/snakemake-wrappers/issues/946))
([ed9ebfb](https://www.github.com/snakemake/snakemake-wrappers/commit/ed9ebfb588af703fe550cf71945ee5b684efa0d8))
* autobump bio/diamond/makedb
([snakemake#944](https://www.github.com/snakemake/snakemake-wrappers/issues/944))
([a95b5db](https://www.github.com/snakemake/snakemake-wrappers/commit/a95b5db5d7c722804b9e4ecb3fa375a76e4f3191))
* autobump bio/gatk/genotypegvcfs
([snakemake#951](https://www.github.com/snakemake/snakemake-wrappers/issues/951))
([5fb96d8](https://www.github.com/snakemake/snakemake-wrappers/commit/5fb96d8e8e43b3350ba2833f291c09d3e7ea1ff0))
* autobump bio/gatk/selectvariants
([snakemake#947](https://www.github.com/snakemake/snakemake-wrappers/issues/947))
([5f697b8](https://www.github.com/snakemake/snakemake-wrappers/commit/5f697b80cf3acee5367efd2fddc58aa7828abba9))
* autobump bio/homer/annotatePeaks
([snakemake#952](https://www.github.com/snakemake/snakemake-wrappers/issues/952))
([8f1270d](https://www.github.com/snakemake/snakemake-wrappers/commit/8f1270de93dd613e1d3f4042ed5c2c3c099b87b5))
* autobump bio/homer/mergePeaks
([snakemake#957](https://www.github.com/snakemake/snakemake-wrappers/issues/957))
([0330a43](https://www.github.com/snakemake/snakemake-wrappers/commit/0330a434160a5a015c19fb76a9c67665ace630ff))
* autobump bio/jellyfish/count
([snakemake#950](https://www.github.com/snakemake/snakemake-wrappers/issues/950))
([0a6f68d](https://www.github.com/snakemake/snakemake-wrappers/commit/0a6f68db8723f2c3f8a794d33badef8e4e32a773))
* autobump bio/last/lastal
([snakemake#942](https://www.github.com/snakemake/snakemake-wrappers/issues/942))
([8e5ef69](https://www.github.com/snakemake/snakemake-wrappers/commit/8e5ef69bc49fc2b911b7b9da6ba8f97c6149590b))
* autobump bio/microphaser/build_reference
([snakemake#943](https://www.github.com/snakemake/snakemake-wrappers/issues/943))
([1e7ece5](https://www.github.com/snakemake/snakemake-wrappers/commit/1e7ece5157bab0a83608a14cbdf45bced50322f0))
* autobump bio/picard/collecttargetedpcrmetrics
([snakemake#949](https://www.github.com/snakemake/snakemake-wrappers/issues/949))
([5239da9](https://www.github.com/snakemake/snakemake-wrappers/commit/5239da9b112d0ad5af6e0f79275b162d9a2b3f57))
* autobump bio/transdecoder/longorfs
([snakemake#956](https://www.github.com/snakemake/snakemake-wrappers/issues/956))
([54c2b74](https://www.github.com/snakemake/snakemake-wrappers/commit/54c2b74e6913cef43fa81a0fd86e997d12c37cde))
* autobump bio/tximport
([snakemake#954](https://www.github.com/snakemake/snakemake-wrappers/issues/954))
([4942f36](https://www.github.com/snakemake/snakemake-wrappers/commit/4942f365b97cabeb7478113aece432d2439ac9ce))
* autobump bio/varscan/somatic
([snakemake#958](https://www.github.com/snakemake/snakemake-wrappers/issues/958))
([28df43c](https://www.github.com/snakemake/snakemake-wrappers/commit/28df43c261751477a9cc888c30794709795e9dcb))
---


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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