Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

feat: Update datavzrd2.18.4 #1292

Merged
merged 4 commits into from Apr 26, 2023
Merged

feat: Update datavzrd2.18.4 #1292

merged 4 commits into from Apr 26, 2023

Conversation

FelixMoelder
Copy link
Contributor

Description

Update datavzrd and allow optional arguments via extra-param

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).

@johanneskoester johanneskoester enabled auto-merge (squash) April 26, 2023 09:41
@johanneskoester johanneskoester enabled auto-merge (squash) April 26, 2023 09:41
@johanneskoester johanneskoester merged commit fa11c1c into master Apr 26, 2023
6 checks passed
@johanneskoester johanneskoester deleted the update_datavzrd2.18.4 branch April 26, 2023 09:42
johanneskoester pushed a commit that referenced this pull request Apr 26, 2023
@github-actions
chore: release 1.27.0 (#1293)
c05e482 
🤖 I have created a release \*beep\* \*boop\*
---
##
[1.27.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v1.26.0...v1.27.0)
(2023-04-26)


### Features

* Update datavzrd to 2.18.4 and add extra params
([#1292](https://www.github.com/snakemake/snakemake-wrappers/issues/1292))
([fa11c1c](https://www.github.com/snakemake/snakemake-wrappers/commit/fa11c1cc37361f879d47ae9dbcf5d7e410003cb1))
---


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>
tgroth97 pushed a commit to tgroth97/snakemake-wrappers that referenced this pull request Apr 27, 2023
@FelixMoelder @johanneskoester @tgroth97
feat: Update datavzrd to 2.18.4 and add extra params (snakemake#1292)
23248e5 
<!-- 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

Update datavzrd and allow optional arguments via `extra`-param

### 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: Johannes Köster <johannes.koester@uni-due.de>
tgroth97 pushed a commit to tgroth97/snakemake-wrappers that referenced this pull request Apr 27, 2023
@github-actions @tgroth97
chore: release 1.27.0 (snakemake#1293)
e270930 
🤖 I have created a release \*beep\* \*boop\*
---
##
[1.27.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v1.26.0...v1.27.0)
(2023-04-26)


### Features

* Update datavzrd to 2.18.4 and add extra params
([snakemake#1292](https://www.github.com/snakemake/snakemake-wrappers/issues/1292))
([fa11c1c](https://www.github.com/snakemake/snakemake-wrappers/commit/fa11c1cc37361f879d47ae9dbcf5d7e410003cb1))
---


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
@FelixMoelder @johanneskoester
feat: Update datavzrd to 2.18.4 and add extra params (snakemake#1292)
1ad26bd 
<!-- 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

Update datavzrd and allow optional arguments via `extra`-param

### 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: Johannes Köster <johannes.koester@uni-due.de>
tdayris pushed a commit to tdayris/snakemake-wrappers that referenced this pull request May 11, 2023
@github-actions
chore: release 1.27.0 (snakemake#1293)
6c9a8d2 
🤖 I have created a release \*beep\* \*boop\*
---
##
[1.27.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v1.26.0...v1.27.0)
(2023-04-26)


### Features

* Update datavzrd to 2.18.4 and add extra params
([snakemake#1292](https://www.github.com/snakemake/snakemake-wrappers/issues/1292))
([fa11c1c](https://www.github.com/snakemake/snakemake-wrappers/commit/fa11c1cc37361f879d47ae9dbcf5d7e410003cb1))
---


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
@FelixMoelder @johanneskoester
feat: Update datavzrd to 2.18.4 and add extra params (snakemake#1292)
f71143a 
<!-- 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

Update datavzrd and allow optional arguments via `extra`-param

### 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: Johannes Köster <johannes.koester@uni-due.de>
tdayris pushed a commit to tdayris/snakemake-wrappers that referenced this pull request Jul 5, 2023
@github-actions
chore: release 1.27.0 (snakemake#1293)
3b31524 
🤖 I have created a release \*beep\* \*boop\*
---
##
[1.27.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v1.26.0...v1.27.0)
(2023-04-26)


### Features

* Update datavzrd to 2.18.4 and add extra params
([snakemake#1292](https://www.github.com/snakemake/snakemake-wrappers/issues/1292))
([fa11c1c](https://www.github.com/snakemake/snakemake-wrappers/commit/fa11c1cc37361f879d47ae9dbcf5d7e410003cb1))
---


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>
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@johanneskoester johanneskoester johanneskoester approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

None yet
2 participants
@FelixMoelder @johanneskoester