Metadata-Version: 1.2
Name: sequana-fastqc
Version: 0.8.1
Summary: A fastqc pipeline from sequana project.
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 **fastqc** pipeline from the `Sequana <https://sequana.readthedocs.org>` projet
        
        :Overview: Runs fastqc and multiqc on a set of Sequencing data to produce control quality reports
        :Input: A set of FastQ files (paired or single-end) compressed or not
        :Output: an HTML file index.html (multiqc) and tree.html (individual fastqc report)
        :Status: production
        
        Usage
        ~~~~~
        
        ::
        
            sequana_pipelines_fastqc --help
            sequana_pipelines_fastqc --input-directory DATAPATH --run-mode local
            sequana_pipelines_fastqc --input-directory DATAPATH --run-mode slurm
        
        This creates a directory **fastq**. You just need to execute the pipeline::
        
            cd fastqc
            sh fastqc.sh  # for a local run
        
        This launch a snakemake pipeline. If you are familiar with snakemake, you can retrieve the fastqc.rules and config.yaml files and then execute the pipeline yourself with specific parameters::
        
            snakemake -s fastqc.rules --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):
        
        - fastqc
        
        .. image:: https://raw.githubusercontent.com/sequana/sequana_fastqc/master/sequana_pipelines/fastqc/dag.png
        
        
        Details
        ~~~~~~~~~
        
        This pipeline runs fastqc in parallel on the input fastq files (paired or not)
        and then execute multiqc. A brief sequana summary report is also produced.
        
        
        Rules and configuration details
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        Here is the `latest documented configuration file <https://raw.githubusercontent.com/sequana/sequana_fastqc/master/sequana_pipelines/fastqc/config.yaml>`_
        to be used with the pipeline. Each rule used in the pipeline may have a section in the configuration file. 
        
        
Keywords: fastqc,NGS,snakemake,multiqc,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 :: 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
