Metadata-Version: 1.2
Name: sequana-revcomp
Version: 0.8.3
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: This is is the **revcomp** pipeline from the `Sequana <https://sequana.readthedocs.org>`_ projet
        
        :Overview: Simply reverse complement a bunch of fastq files
        :Input: fastq files
        :Output: their reverse complement counterpart
        :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
        
        
        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/master/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/master/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
        ========= ======================================================================
        0.8.3     * 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 :: 3.5
Classifier: Programming Language :: Python :: 3.6
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
