Sequana Sphinxext
| 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
