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.

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

feat: Add threads to cooltools insulation #919

Merged
merged 1 commit into from Nov 28, 2022
Merged

Conversation

Phlya
Copy link
Contributor

@Phlya Phlya commented Nov 22, 2022

Description

Recent release of cooltools allows multiple threads in the insulation command, now the wrapper passes the snakemake.threads to the -p argument.

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 Add threads to cooltools insulation feat: Add threads to cooltools insulation Nov 22, 2022
@fgvieira fgvieira merged commit fdf035e into snakemake:master Nov 28, 2022
@Phlya
Copy link
Contributor Author

Phlya commented Nov 28, 2022

Thanks @fgvieira !

johanneskoester pushed a commit that referenced this pull request Dec 1, 2022
🤖 I have created a release \*beep\* \*boop\*
---
##
[1.20.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v1.19.2...v1.20.0)
(2022-12-01)


### Features

* Add threads to cooltools insulation
([#919](https://www.github.com/snakemake/snakemake-wrappers/issues/919))
([fdf035e](https://www.github.com/snakemake/snakemake-wrappers/commit/fdf035ea037d7ce3c2883d49d76fd186e350bbac))
* GATK SplitIntervals wrapper
([#836](https://www.github.com/snakemake/snakemake-wrappers/issues/836))
([986fa3a](https://www.github.com/snakemake/snakemake-wrappers/commit/986fa3a4f330cf0ff27869718a17aa86668ca141))
* samtools view allow region specification
([#940](https://www.github.com/snakemake/snakemake-wrappers/issues/940))
([c1fdb5e](https://www.github.com/snakemake/snakemake-wrappers/commit/c1fdb5eab1496b5e95a4a8ede82670cf2f6d2cef))


### Bug Fixes

* Correct referencing of Snakemake input variables (release: 1.19.2)
([#937](https://www.github.com/snakemake/snakemake-wrappers/issues/937))
([b828ac3](https://www.github.com/snakemake/snakemake-wrappers/commit/b828ac3c6eaf5c8382e3746635817cebcefe449f))


### Performance Improvements

* autobump bio/bowtie2/build
([#932](https://www.github.com/snakemake/snakemake-wrappers/issues/932))
([26bcc0b](https://www.github.com/snakemake/snakemake-wrappers/commit/26bcc0b2ec6b553fc6c0720d9075c4def2de2ef5))
* autobump bio/dada2/learn-errors
([#929](https://www.github.com/snakemake/snakemake-wrappers/issues/929))
([32e9f5c](https://www.github.com/snakemake/snakemake-wrappers/commit/32e9f5c15442f78978b319205ed2b517a14e3f3a))
* autobump bio/gatk/baserecalibratorspark
([#935](https://www.github.com/snakemake/snakemake-wrappers/issues/935))
([ff15e44](https://www.github.com/snakemake/snakemake-wrappers/commit/ff15e44badd984d4dd6598bafa41d93959c8afb0))
* autobump bio/gatk/cleansam
([#792](https://www.github.com/snakemake/snakemake-wrappers/issues/792))
([6055e79](https://www.github.com/snakemake/snakemake-wrappers/commit/6055e791c104c896f18d3671f3593ad83340d6e7))
* autobump bio/gatk/estimatelibrarycomplexity
([#926](https://www.github.com/snakemake/snakemake-wrappers/issues/926))
([c366755](https://www.github.com/snakemake/snakemake-wrappers/commit/c3667553c4354932bb7efdbfca0587f7b205b42e))
* autobump bio/infernal/cmscan
([#924](https://www.github.com/snakemake/snakemake-wrappers/issues/924))
([36634d9](https://www.github.com/snakemake/snakemake-wrappers/commit/36634d91f686e03385e5af5de1c7fe1cbf1c0ea5))
* autobump bio/microphaser/somatic
([#925](https://www.github.com/snakemake/snakemake-wrappers/issues/925))
([cb44ee0](https://www.github.com/snakemake/snakemake-wrappers/commit/cb44ee09dafa8bb51a449a42d325a8523a8c27fc))
* autobump bio/picard/collectinsertsizemetrics
([#934](https://www.github.com/snakemake/snakemake-wrappers/issues/934))
([fd8fecd](https://www.github.com/snakemake/snakemake-wrappers/commit/fd8fecdcd9db0994686219f45307b62b27bb5a85))
* autobump bio/picard/collectrnaseqmetrics
([#920](https://www.github.com/snakemake/snakemake-wrappers/issues/920))
([40eccd5](https://www.github.com/snakemake/snakemake-wrappers/commit/40eccd5ae9e5ac0814a448b6ccb3917f4c35b28d))
* autobump bio/pretext/graph
([#930](https://www.github.com/snakemake/snakemake-wrappers/issues/930))
([2a1fb56](https://www.github.com/snakemake/snakemake-wrappers/commit/2a1fb569f7e9e0b5afe515ffb24cfe82f11f64ae))
* autobump bio/purge_dups/get_seqs
([#922](https://www.github.com/snakemake/snakemake-wrappers/issues/922))
([ad5fba2](https://www.github.com/snakemake/snakemake-wrappers/commit/ad5fba20ed453cd0c8ce7222481f2cf425e4d460))
* autobump bio/samtools/sort
([#921](https://www.github.com/snakemake/snakemake-wrappers/issues/921))
([4dde2ae](https://www.github.com/snakemake/snakemake-wrappers/commit/4dde2ae49115171502f1f0a162b24bfa8eebb5db))
* autobump bio/samtools/view
([#936](https://www.github.com/snakemake/snakemake-wrappers/issues/936))
([24254fd](https://www.github.com/snakemake/snakemake-wrappers/commit/24254fdf65866b09a52feeb307943c633d875959))
* autobump bio/vembrane/filter
([#927](https://www.github.com/snakemake/snakemake-wrappers/issues/927))
([510b06a](https://www.github.com/snakemake/snakemake-wrappers/commit/510b06af5e32befd649da3f9340b716665c9b6e0))
* autobump bio/vep/annotate
([#928](https://www.github.com/snakemake/snakemake-wrappers/issues/928))
([bb30b19](https://www.github.com/snakemake/snakemake-wrappers/commit/bb30b19d1df00ac89f124a3a8ee93530ed2285c5))
* autobump bio/vg/kmers
([#931](https://www.github.com/snakemake/snakemake-wrappers/issues/931))
([067b6a8](https://www.github.com/snakemake/snakemake-wrappers/commit/067b6a8735ff09cbfeacdd1478f034b3e24433e5))
* autobump bio/vg/merge
([#933](https://www.github.com/snakemake/snakemake-wrappers/issues/933))
([5ac344d](https://www.github.com/snakemake/snakemake-wrappers/commit/5ac344d929e147fc9c450792b2438a83bbd3b633))
* update to latest datavzrd
([d08bc08](https://www.github.com/snakemake/snakemake-wrappers/commit/d08bc08197e925c9b3e96d53bed453153cc9576f))
---


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

Recent release of cooltools allows multiple threads in the insulation
command, now the wrapper passes the snakemake.threads to the -p
argument.

### 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\*
---
##
[1.20.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v1.19.2...v1.20.0)
(2022-12-01)


### Features

* Add threads to cooltools insulation
([snakemake#919](https://www.github.com/snakemake/snakemake-wrappers/issues/919))
([fdf035e](https://www.github.com/snakemake/snakemake-wrappers/commit/fdf035ea037d7ce3c2883d49d76fd186e350bbac))
* GATK SplitIntervals wrapper
([snakemake#836](https://www.github.com/snakemake/snakemake-wrappers/issues/836))
([986fa3a](https://www.github.com/snakemake/snakemake-wrappers/commit/986fa3a4f330cf0ff27869718a17aa86668ca141))
* samtools view allow region specification
([snakemake#940](https://www.github.com/snakemake/snakemake-wrappers/issues/940))
([c1fdb5e](https://www.github.com/snakemake/snakemake-wrappers/commit/c1fdb5eab1496b5e95a4a8ede82670cf2f6d2cef))


### Bug Fixes

* Correct referencing of Snakemake input variables (release: 1.19.2)
([snakemake#937](https://www.github.com/snakemake/snakemake-wrappers/issues/937))
([b828ac3](https://www.github.com/snakemake/snakemake-wrappers/commit/b828ac3c6eaf5c8382e3746635817cebcefe449f))


### Performance Improvements

* autobump bio/bowtie2/build
([snakemake#932](https://www.github.com/snakemake/snakemake-wrappers/issues/932))
([26bcc0b](https://www.github.com/snakemake/snakemake-wrappers/commit/26bcc0b2ec6b553fc6c0720d9075c4def2de2ef5))
* autobump bio/dada2/learn-errors
([snakemake#929](https://www.github.com/snakemake/snakemake-wrappers/issues/929))
([32e9f5c](https://www.github.com/snakemake/snakemake-wrappers/commit/32e9f5c15442f78978b319205ed2b517a14e3f3a))
* autobump bio/gatk/baserecalibratorspark
([snakemake#935](https://www.github.com/snakemake/snakemake-wrappers/issues/935))
([ff15e44](https://www.github.com/snakemake/snakemake-wrappers/commit/ff15e44badd984d4dd6598bafa41d93959c8afb0))
* autobump bio/gatk/cleansam
([snakemake#792](https://www.github.com/snakemake/snakemake-wrappers/issues/792))
([6055e79](https://www.github.com/snakemake/snakemake-wrappers/commit/6055e791c104c896f18d3671f3593ad83340d6e7))
* autobump bio/gatk/estimatelibrarycomplexity
([snakemake#926](https://www.github.com/snakemake/snakemake-wrappers/issues/926))
([c366755](https://www.github.com/snakemake/snakemake-wrappers/commit/c3667553c4354932bb7efdbfca0587f7b205b42e))
* autobump bio/infernal/cmscan
([snakemake#924](https://www.github.com/snakemake/snakemake-wrappers/issues/924))
([36634d9](https://www.github.com/snakemake/snakemake-wrappers/commit/36634d91f686e03385e5af5de1c7fe1cbf1c0ea5))
* autobump bio/microphaser/somatic
([snakemake#925](https://www.github.com/snakemake/snakemake-wrappers/issues/925))
([cb44ee0](https://www.github.com/snakemake/snakemake-wrappers/commit/cb44ee09dafa8bb51a449a42d325a8523a8c27fc))
* autobump bio/picard/collectinsertsizemetrics
([snakemake#934](https://www.github.com/snakemake/snakemake-wrappers/issues/934))
([fd8fecd](https://www.github.com/snakemake/snakemake-wrappers/commit/fd8fecdcd9db0994686219f45307b62b27bb5a85))
* autobump bio/picard/collectrnaseqmetrics
([snakemake#920](https://www.github.com/snakemake/snakemake-wrappers/issues/920))
([40eccd5](https://www.github.com/snakemake/snakemake-wrappers/commit/40eccd5ae9e5ac0814a448b6ccb3917f4c35b28d))
* autobump bio/pretext/graph
([snakemake#930](https://www.github.com/snakemake/snakemake-wrappers/issues/930))
([2a1fb56](https://www.github.com/snakemake/snakemake-wrappers/commit/2a1fb569f7e9e0b5afe515ffb24cfe82f11f64ae))
* autobump bio/purge_dups/get_seqs
([snakemake#922](https://www.github.com/snakemake/snakemake-wrappers/issues/922))
([ad5fba2](https://www.github.com/snakemake/snakemake-wrappers/commit/ad5fba20ed453cd0c8ce7222481f2cf425e4d460))
* autobump bio/samtools/sort
([snakemake#921](https://www.github.com/snakemake/snakemake-wrappers/issues/921))
([4dde2ae](https://www.github.com/snakemake/snakemake-wrappers/commit/4dde2ae49115171502f1f0a162b24bfa8eebb5db))
* autobump bio/samtools/view
([snakemake#936](https://www.github.com/snakemake/snakemake-wrappers/issues/936))
([24254fd](https://www.github.com/snakemake/snakemake-wrappers/commit/24254fdf65866b09a52feeb307943c633d875959))
* autobump bio/vembrane/filter
([snakemake#927](https://www.github.com/snakemake/snakemake-wrappers/issues/927))
([510b06a](https://www.github.com/snakemake/snakemake-wrappers/commit/510b06af5e32befd649da3f9340b716665c9b6e0))
* autobump bio/vep/annotate
([snakemake#928](https://www.github.com/snakemake/snakemake-wrappers/issues/928))
([bb30b19](https://www.github.com/snakemake/snakemake-wrappers/commit/bb30b19d1df00ac89f124a3a8ee93530ed2285c5))
* autobump bio/vg/kmers
([snakemake#931](https://www.github.com/snakemake/snakemake-wrappers/issues/931))
([067b6a8](https://www.github.com/snakemake/snakemake-wrappers/commit/067b6a8735ff09cbfeacdd1478f034b3e24433e5))
* autobump bio/vg/merge
([snakemake#933](https://www.github.com/snakemake/snakemake-wrappers/issues/933))
([5ac344d](https://www.github.com/snakemake/snakemake-wrappers/commit/5ac344d929e147fc9c450792b2438a83bbd3b633))
* update to latest datavzrd
([d08bc08](https://www.github.com/snakemake/snakemake-wrappers/commit/d08bc08197e925c9b3e96d53bed453153cc9576f))
---


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
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

None yet

2 participants