Metadata-Version: 1.2
Name: sequana-ribofinder
Version: 0.10.1
Summary: NGS, ribosomal, rRNA, snakemake, sequana
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-ribofinder.svg
             :target: https://pypi.python.org/pypi/sequana_ribofinder
        
        .. 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/ribofinder/actions/workflows/main.yml/badge.svg
           :target: https://github.com/sequana/ribofinder/actions/workflows    
        
        
        This is is the **ribofinder** pipeline from the `Sequana <https://sequana.readthedocs.org>`_ project
        
        :Overview: Simple parallele workflow to detect and report ribosomal content
        :Input: FastQ files
        :Output: HTML reports
        :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
        ~~~~~~~~~~~~
        
        You must install Sequana first (use --upgrade to get the latest version installed)::
        
            pip install sequana --upgrade
        
        Then, just install this package::
        
            pip install sequana_ribofinder --upgrade
        
        Usage
        ~~~~~
        
        
        This command will scan all files ending in .fastq.gz found in the local
        directory, create a directory called fastqc/ where a snakemake pipeline is
        launched automatically. Depending on the number of files and their sizes, the
        process may be long::
        
            sequana_pipelines_ribofinder --help
            sequana_pipelines_ribofinder --input-directory DATAPATH 
        
        This creates a directory with the pipeline and configuration file. You will then need 
        to execute the pipeline::
        
            cd ribofinder
            sh ribofinder.sh  # for a local run
        
        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 ribofinder.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):
        
        - bowtie1
        
        .. image:: https://raw.githubusercontent.com/sequana/ribofinder/master/sequana_pipelines/ribofinder/dag.png
        
        
        Details
        ~~~~~~~~~
        
        This pipeline runs **ribofinder** in parallel on the input fastq files. 
        A brief sequana summary report is also produced.
        
        
        Rules and configuration details
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        Here is the `latest documented configuration file <https://raw.githubusercontent.com/sequana/ribofinder/master/sequana_pipelines/ribofinder/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
        ========= ====================================================================
        0.10.1    * add additional test and fix bug in pipeline (regression bug)
        0.10.0    * Update to use sequana-wrappers. Remove multiqc. summary.html 
                    is self-content
        0.9.3     * fix logger
        0.9.2     **First release.**
        ========= ====================================================================
        
        
        
Keywords: NGS, ribosomal, rRNA, snakemake, 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
