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feat: Rseqc infer experiment #2730
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* perf: update bio/bcftools/index/environment.yaml. * perf: update bio/bcftools/index/environment.yaml. * perf: update bio/bcftools/index/environment.yaml.
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* Add autobump action * fix paths * dbg * dbg branch * add checkout * dbg * trigger rerun * entity regex and add label * dbg * Update autobump.yml * Update autobump.yml
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Automatic update of bio/deepvariant. Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com> Co-authored-by: Johannes Köster <johannes.koester@uni-due.de>
<!-- 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).
🤖 I have created a release \*beep\* \*boop\* --- ## [1.16.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v1.15.2...v1.16.0) (2022-10-13) ### Features * bazam wrapper ([snakemake#580](https://www.github.com/snakemake/snakemake-wrappers/issues/580)) ([17e58e6](https://www.github.com/snakemake/snakemake-wrappers/commit/17e58e6f254ce429b3b76b841df29b573949e278)) ### Bug Fixes * set RG tag ([snakemake#593](https://www.github.com/snakemake/snakemake-wrappers/issues/593)) ([506a083](https://www.github.com/snakemake/snakemake-wrappers/commit/506a08391b56d4b53edda2c6555b9b9d404d4f94)) ### Performance Improvements * autobump bio/deepvariant ([snakemake#583](https://www.github.com/snakemake/snakemake-wrappers/issues/583)) ([9b7c4fe](https://www.github.com/snakemake/snakemake-wrappers/commit/9b7c4feec69d05fc7d6286dcdfdc65802cb93317)) --- 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>
fgvieira
reviewed
Mar 8, 2024
…nakemake-wrappers into rseqc_infer_experiment
fgvieira
approved these changes
Mar 8, 2024
johanneskoester
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Mar 13, 2024
🤖 I have created a release \*beep\* \*boop\* --- ## [3.5.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v3.4.1...v3.5.0) (2024-03-13) ### Features * Genepred to bed ([#2726](https://www.github.com/snakemake/snakemake-wrappers/issues/2726)) ([3998574](https://www.github.com/snakemake/snakemake-wrappers/commit/3998574d4c3cc02706ef4056dbb387835755e0f6)) * MultiQC automatically detects configuration from input file(s) ([#2722](https://www.github.com/snakemake/snakemake-wrappers/issues/2722)) ([f61238d](https://www.github.com/snakemake/snakemake-wrappers/commit/f61238d350ba737aae0b2948857d7f50d5f124d7)) * Rseqc distribution ([#2737](https://www.github.com/snakemake/snakemake-wrappers/issues/2737)) ([c732ff0](https://www.github.com/snakemake/snakemake-wrappers/commit/c732ff0c1fc5e139659a65c5b4495c67a1476985)) * Rseqc infer experiment ([#2730](https://www.github.com/snakemake/snakemake-wrappers/issues/2730)) ([c597f2b](https://www.github.com/snakemake/snakemake-wrappers/commit/c597f2b50170ef0f3843624b38beb27f644022cc)) * Rseqc read duplication ([#2731](https://www.github.com/snakemake/snakemake-wrappers/issues/2731)) ([2d5f9e7](https://www.github.com/snakemake/snakemake-wrappers/commit/2d5f9e79b6620cd2bc4627c643b0db846e4d576d)) * Rseqc read gc ([#2729](https://www.github.com/snakemake/snakemake-wrappers/issues/2729)) ([739d809](https://www.github.com/snakemake/snakemake-wrappers/commit/739d809ad6d85a17bc5028a549d1e9e1b5262568)) * run Mutect2 multiple with input bam files ([#2736](https://www.github.com/snakemake/snakemake-wrappers/issues/2736)) ([7b42689](https://www.github.com/snakemake/snakemake-wrappers/commit/7b426894a935eb071a842176e2449d481edf6d6c)) ### Performance Improvements * autobump bio/gseapy/gsea ([#2727](https://www.github.com/snakemake/snakemake-wrappers/issues/2727)) ([400db30](https://www.github.com/snakemake/snakemake-wrappers/commit/400db30891d291605d7bb9e039937a62aea23107)) * autobump bio/sra-tools/fasterq-dump ([#2728](https://www.github.com/snakemake/snakemake-wrappers/issues/2728)) ([92c9521](https://www.github.com/snakemake/snakemake-wrappers/commit/92c952124f885624e7725b672f8926cfb7386f76)) * Update Datavzrd ([#2735](https://www.github.com/snakemake/snakemake-wrappers/issues/2735)) ([41b562c](https://www.github.com/snakemake/snakemake-wrappers/commit/41b562cf1c387294e7637e46cce66dd2bcb6218e)) * Update Datavzrd to 2.36.4 ([#2720](https://www.github.com/snakemake/snakemake-wrappers/issues/2720)) ([7611d30](https://www.github.com/snakemake/snakemake-wrappers/commit/7611d30950b85360cb91ff2b58895ae788e05c68)) * Update Datavzrd to 2.36.5 ([#2733](https://www.github.com/snakemake/snakemake-wrappers/issues/2733)) ([2fad8a1](https://www.github.com/snakemake/snakemake-wrappers/commit/2fad8a1bdf205033b799ce0048aae5af6c2b57c1)) * Update Datavzrd to 2.36.8 ([#2738](https://www.github.com/snakemake/snakemake-wrappers/issues/2738)) ([8c86447](https://www.github.com/snakemake/snakemake-wrappers/commit/8c86447fde4419e377e7a2c544a330343bbf19ab)) --- 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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This PR adds RSeQC infer_experiment.py to the list of available wrappers.
This is an example of "very simple" wrappers I was talking about in the PR on
read_gc.py
.QC
For all wrappers added by this PR,
input:
andoutput:
file paths in the resulting rule can be changed arbitrarily,threads: x
statement withx
being a reasonable default,map_reads
for a step that maps reads),environment.yaml
specifications follow the respective best practices,environment.yaml
pinning has been updated by runningsnakedeploy pin-conda-envs environment.yaml
on a linux machine,input:
oroutput:
),Snakefile
s and their entries are explained via comments (input:
/output:
/params:
etc.),stderr
and/orstdout
are logged correctly (log:
), depending on the wrapped tool,tempfile.gettempdir()
points to (see here; this also means that using any Pythontempfile
default behavior works),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,