.. image:: https://badge.fury.io/py/sequana-revcomp.svg
:target: https://pypi.python.org/pypi/sequana_revcomp
.. 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
.. image:: https://github.com/sequana/revcomp/actions/workflows/main.yml/badge.svg
:target: https://github.com/sequana/revcomp/actions/workflows
.. image:: https://img.shields.io/badge/python-3.8%20%7C%203.9%20%7C3.10-blue.svg
:target: https://pypi.python.org/pypi/sequana
:alt: Python 3.8 | 3.9 | 3.10
This is is the **revcomp** pipeline from the `Sequana <https://sequana.readthedocs.org>`_ projet
:Overview: revert and complement input Fast files
:Input: A set of FastQ files (paired or single-end) compressed or not
:Output: A set of reverse completed files
:Status: production
:Citation: 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
Installation
~~~~~~~~~~~~
If you already have all requirements, you can install the packages using pip::
pip install sequana_mapper --upgrade
Usage
~~~~~
::
sequana_revcomp --input-directory DATAPATH
This creates a directory with the pipeline and configuration file. You will then need
to execute the pipeline::
cd revcomp
sh revcomp.sh # for a local run
make clean
This launch a snakemake pipeline. If you are familiar with snakemake, you can
retrieve the pipeline itself and its configuration files and then execute the pipeline yourself with specific parameters::
snakemake -s revcomp.rules -c config.yaml --cores 4 \
--wrapper-prefix https://raw.githubusercontent.com/sequana/sequana-wrappers/
Or use `sequanix <https://sequana.readthedocs.io/en/main/sequanix.html>`_ interface.
Requirements
~~~~~~~~~~~~
This pipelines requires the following executable(s):
- seqtk
Details
~~~~~~~~~
This pipeline runs **seqtk** in parallel on the input fastq files.
Rules and configuration details
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Here is the `latest documented configuration file <https://raw.githubusercontent.com/sequana/sequana_revcomp/main/sequana_pipelines/revcomp/config.yaml>`_
to be used with the pipeline. Each rule used in the pipeline may have a section in the configuration file.
Changelog
~~~~~~~~~
========= ======================================================================
Version Description
========= ======================================================================
0.9.0 * set singularity container
0.8.4 * implemented --from-project option
0.8.3 * Uses new sequana framework to spee up --help calls
* --threads option
0.8.2 Fix schema and rule. output files are now saved in the ./rc directory
0.8.1 Improve the --help message
0.8.0 First version from sequana 0.8.0
========= ======================================================================
Raw data
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