Metadata-Version: 1.2
Name: sequana-revcomp
Version: 1.0.0
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
Description: 
        .. 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
        ========= ======================================================================
        
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 :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
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
