sequana-sphinxext 1.0.0

A set of sphinx extension for Sequana pipelines, wrappers and rules

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