Metadata-Version: 2.1
Name: sequana-bioconvert
Version: 1.0.0
Summary: description: convert NGS format from one to another using bioconvert
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: |Logo|
        
        
        This is is the **bioconvert** pipeline from the `Sequana <https://sequana.readthedocs.org>`_ project
        
        
        .. image:: https://badge.fury.io/py/sequana-bioconvert.svg
             :target: https://pypi.python.org/pypi/sequana_bioconvert
        
        .. 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/bioconvert/actions/workflows/main.yml/badge.svg
           :target: https://github.com/sequana/bioconvert/actions/workflows    
        
        |Codacy-Grade|
        
        
        :Overview: convert NGS format from one to another using Bioconvert
        :Input: whatever input format accepted by Bioconvert
        :Output: whatever output format accepted by Bioconvert
        :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
        ~~~~~~~~~~~~
        
        This package depends on Python only and singularity. To install **sequana_bioconvert**, just install this package as
        follows::
        
            pip install sequana_bioconvert
        
        For **singularity**, we recommend to use a conda environment::
        
        
            conda create --name bioconvert -y python=3.8 singularity
            conda activate bioconvert
            pip install sequana_bioconvert
        
        
        Usage
        ~~~~~
        
        ::
        
            sequana_bioconvert --help
        
        You need to provide the type of conversion you wish to perform with the
        *--command* argument. You also need to tell the type of extensions expected
        including the compression (gz, bz2 or dsrc recognised). Finally, the
        *--input-directory* and *--input-pattern* must be used to find the input
        files.::
        
            sequana_bioconvert --input-directory . --input-ext fastq.gz --output-ext
                fasta.gz --command fastq2fasta --input-pattern "*.fastq.gz"
        
        This command creates a directory with the pipeline and configuration file. You will then need 
        to execute the pipeline as follows::
        
            cd bioconvert
            sh bioconvert.sh  # for a local run
        
        This launches a snakemake pipeline. Symbolic links to the input data are created in
        the ./input directory and results stored in the ./output directory.
        
        Some conversions require external standalones. We recommend to use our singularity image. 
        To do so, add **--use-apptainer** options when you initialse the pipeline. You can also 
        specify where to store the singularity image once for all using **--apptainer-prefix**::
        
            sequana_bioconvert --input-directory . --input-ext fastq.gz --output-ext
                fasta.gz --command fastq2fasta --input-pattern "*.fastq.gz"
                --use-apptainer --apptainer-prefix ~/images
        
        
        See bioconvert.readthedocs.io for more details about **bioconvert** itself.
        
        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 bioconvert.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) installed with sequana_bioconvert: bioconvert
        
        All dependencies and external dependencies related to bioconvert are available through the apptainer used by this
        **sequana_bioconvert** pipeline. 
        
        
        
        Rules and configuration details
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        Here is the `latest documented configuration file <https://raw.githubusercontent.com/sequana/sequana_bioconvert/main/sequana_pipelines/bioconvert/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
        ========= ====================================================================
        1.0.0     Uses bioconvert 1.0.0
        0.10.0    Add container
        0.9.0     Version using new sequana/sequana_pipetools framework
        0.8.1     **Working version**
        0.8.0     **First release.**
        ========= ====================================================================
        
        
        Contribute & Code of Conduct
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        To contribute to this project, please take a look at the 
        `Contributing Guidelines <https://github.com/sequana/sequana/blob/main/CONTRIBUTING.rst>`_ first. Please note that this project is released with a 
        `Code of Conduct <https://github.com/sequana/sequana/blob/main/CONDUCT.md>`_. By contributing to this project, you agree to abide by its terms.
        
        
        .. |Codacy-Grade| image:: https://app.codacy.com/project/badge/Grade/9b8355ff642f4de9acd4b270f8d14d10
           :target: https://www.codacy.com/gh/sequana/bioconvert/dashboard
        
        .. |Logo| image:: https://github.com/sequana/sequana/blob/dev/doc/_static/logo_256x256.png
        
Keywords: NGS,snakemake,bioconvert,conversion,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
Provides-Extra: testing
