Metadata-Version: 2.1
Name: sequana-revcomp
Version: 0.9.0
Summary: reverse complement a set of FastQ files
Home-page: https://github.com/sequana/
Author: thomas cokelaer
Author-email: thomas.cokelaer@pasteur.fr
Maintainer: thomas cokelaer
Maintainer-email: thomas.cokelaer@pasteur.fr
License: new BSD
Keywords: fastq, reverse complement, snakemake, NGS,sequana
Platform: Linux
Platform: Unix
Platform: MacOsX
Platform: Windows
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Education
Classifier: Intended Audience :: End Users/Desktop
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Information Analysis
Classifier: Topic :: Scientific/Engineering :: Mathematics
Classifier: Topic :: Scientific/Engineering :: Physics
License-File: LICENSE


.. 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    



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
:Authors: Thomas Cokelaer



This is is the **fastqc** pipeline from the `Sequana <https://sequana.readthedocs.org>`_ projet

:Overview: Runs fastqc and multiqc on a set of Sequencing data to produce control quality reports
:Input: A set of FastQ files (paired or single-end) compressed or not
:Output: an HTML file summary.html (individual fastqc reports, mutli-samples report)
:Status: production
:Wiki: https://github.com/sequana/fastqc/wiki
:Documentation: This README file, the Wiki from the github repository (link above) and https://sequana.readthedocs.io
:Citation: Cokelaer et al, (2017), 'Sequana': a Set of Snakemake NGS pipelines, Journal of Open Source Software, 2(16), 352, JOSS DOI https://doi:10.21105/joss.00352


Installation
~~~~~~~~~~~~

You must install Sequana first::

    pip install sequana

Then, just install this package::

    pip install sequana_revcomp


Usage
~~~~~

::

    sequana_pipelines_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 --stats stats.txt

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
========= ======================================================================
0.8.4     * 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
========= ======================================================================


