Metadata-Version: 1.2
Name: sequana-ribofinder
Version: 0.13.0
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/main.yml
        
        
        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
        ~~~~~~~~~~~~
        
        Using **pip** from Python, just install this package::
        
            pip install sequana_ribofinder --upgrade
        
        The **--upgrade** option is to make sure you'll get the latest version.
        
        Usage
        ~~~~~
        
        This pipeline scans input fastq.gz files found in the local
        directory and identify the proportion of ribosomal content.
        
        For help, please type::
        
            sequana_ribofinder --help
        
        The following command searches for input files in DATAPATH. Then, te user provide
        a list of rRNA sequences in FastA format in *test.fasta*. This command creates a directory 
        called ribofinder/ where a snakemake pipeline can::
        
            sequana_ribofinder --input-directory DATAPATH --rRNA-file test.fasta
        
        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 --wrapper-prefix git+file:////home/user/sequana_wrappers
        
        
        Or use `sequanix <https://sequana.readthedocs.io/en/master/sequanix.html>`_ interface.
        
        Requirements
        ~~~~~~~~~~~~
        
        This pipelines requires the following executable(s):
        
        - bowtie1 >= 1.3.0
        - bedtools
        - samtools
        - bamtools
        - pigz
        
        .. 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.
        
        You can start from the reference file and the GFF file. By default we search for the feature called 
        rRNA to be found in the GFF file::
        
            sequana_ribofinder --input-directory . --reference-file genome.fasta --gff-file genome.gff
        
        If the default feature rRNA is not found, no error is raised for now. If you know the expected feature, 
        you can provide it though::
        
            sequana_ribofinder --input-directory . --reference-file genome.fasta --gff-file genome.gff --rRNA-feature gene_rRNA
        
        If you have an existing or custom rRNA file, you can then use it as follows, in which case, no input reference is
        required::
        
            sequana_ribofinder --input-directory . --rRNA-file ribo.fasta
        
        
        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
        ========= ====================================================================
        0.13.0    * add  final apptainers and update CI actions
        0.12.0    * set singularity containers
        0.11.1    * Fix config file (removing hard-coded path)
        0.11.0    * Fix multiqc plot using same fix as in sequna_rnaseq pipelines
                  * add utility plot to check rate of  ribosomal per sequence and also
                    the corresponding  RPKM.
        0.10.2    * Fix the bowtie1 rule (all samples were named bowtie1)
        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
