https://github.com/sequana/sequana_sphinxext
sphinx extensions for sequana documentation
https://github.com/sequana/sequana_sphinxext
Last synced: 8 months ago
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sphinx extensions for sequana documentation
- Host: GitHub
- URL: https://github.com/sequana/sequana_sphinxext
- Owner: sequana
- Created: 2021-08-10T18:09:11.000Z (almost 5 years ago)
- Default Branch: master
- Last Pushed: 2021-11-24T12:48:38.000Z (over 4 years ago)
- Last Synced: 2025-01-25T13:46:23.802Z (over 1 year ago)
- Language: Python
- Size: 59.6 KB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.rst
Awesome Lists containing this project
README
Sequana Sphinxext
##################
.. image:: https://badge.fury.io/py/sequana-sphinxext.svg
:target: https://pypi.python.org/pypi/sequana-sphinxext
.. image:: https://github.com/sequana/sequana_sphinxext/actions/workflows/main.yml/badge.svg?branch=master
:target: https://github.com/sequana/sequana_sphinext/actions/workflows/main.yml
.. image:: https://coveralls.io/repos/github/sequana/sequana_sphinxext/badge.svg?branch=master
:target: https://coveralls.io/github/sequana/sequana_sphinxext?branch=master
.. image:: http://joss.theoj.org/papers/10.21105/joss.00352/status.svg
:target: http://joss.theoj.org/papers/10.21105/joss.00352
:alt: JOSS (journal of open source software) DOI
:Python version: 3.7.3, 3.8 ,3.9
:Status: Production
:Issues: Please fill issues `On github `_
:How to cite: Citations are important for us to carry on developments.
For Sequana library (including the pipelines), please use
Cokelaer et al, (2017), 'Sequana': a Set of Snakemake NGS pipelines, Journal of
Open Source Software, 2(16), 352, `JOSS DOI doi:10.21105/joss.00352 `_
The sequana_sphinxext package is used exclusively to provide Sphinx extensions for the Sequana
project. **Sequana** includes a set of pipelines related to NGS (new generation sequencing) including quality control, variant calling, coverage, taxonomy, transcriptomics. **Please see the** `documentation `_ for an up-to-date status.
We have three sphinx extension to be added in your Sphinx configuration files in the extensions list::
extensions += [
"sequana_sphinxext.snakemakerule",
"sequana_sphinxext.pipeline",
"sequana_sphinxext.wrapper"]
You can then include a wrapper from `sequana wrappers `_ using e.g.::
.. sequana_wrapper:: fastqc
or a rule from Sequana::
.. snakemakerule:: fastq_sampling
or a pipeline from sequana::
.. sequana_pipeline:: demultiplex