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Sphinxext\n##################\n\n\n.. image:: https://badge.fury.io/py/sequana-sphinxext.svg\n    :target: https://pypi.python.org/pypi/sequana-sphinxext\n\n.. image:: https://github.com/sequana/sequana_sphinxext/actions/workflows/main.yml/badge.svg?branch=master\n    :target: https://github.com/sequana/sequana_sphinext/actions/workflows/main.yml\n\n.. image:: https://coveralls.io/repos/github/sequana/sequana_sphinxext/badge.svg?branch=master\n    :target: https://coveralls.io/github/sequana/sequana_sphinxext?branch=master \n\n.. image:: http://joss.theoj.org/papers/10.21105/joss.00352/status.svg\n   :target: http://joss.theoj.org/papers/10.21105/joss.00352\n   :alt: JOSS (journal of open source software) DOI\n\n\n:Python version:  3.7.3, 3.8 ,3.9\n:Status: Production\n:Issues: Please fill issues `On github \u003chttps://github.com/sequana/sequana/issues\u003e`_\n:How to cite: Citations are important for us to carry on developments.\n    For Sequana library (including the pipelines), please use\n\n    Cokelaer et al, (2017), 'Sequana': a Set of Snakemake NGS pipelines, Journal of\n    Open Source Software, 2(16), 352, `JOSS DOI doi:10.21105/joss.00352 \u003chttps://joss.theoj.org/papers/10.21105/joss.00352\u003e`_\n \n\nThe sequana_sphinxext  package is used exclusively to provide Sphinx extensions for the Sequana\nproject. **Sequana** includes a set of pipelines related to NGS (new generation sequencing) including quality control, variant calling, coverage, taxonomy, transcriptomics. **Please see the** `documentation \u003chttp://sequana.readthedocs.org\u003e`_ for an up-to-date status.\n\nWe have three sphinx extension to be added in your Sphinx configuration files in the extensions list::\n\n    extensions += [\n        \"sequana_sphinxext.snakemakerule\",\n        \"sequana_sphinxext.pipeline\",\n        \"sequana_sphinxext.wrapper\"]\n\nYou can then include a wrapper from  `sequana wrappers \u003chttps://github.com/sequana/sequana-wrappers\u003e`_ using e.g.::\n\n    .. sequana_wrapper:: fastqc\n\nor a rule from Sequana::\n\n    .. snakemakerule:: fastq_sampling\n\nor a pipeline from sequana::\n\n    .. sequana_pipeline:: demultiplex\n\n\n\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsequana%2Fsequana_sphinxext","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsequana%2Fsequana_sphinxext","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsequana%2Fsequana_sphinxext/lists"}