Metadata-Version: 1.2
Name: sequana-fastqc
Version: 0.9.10
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
        :Citation: Cokelaer et al, (2017), 'Sequana': a Set of Snakemake NGS pipelines, Journal of Open Source Software, 2(16), 352, JOSS DOI https://doi:10.21105/joss.00352
        
        
        Installation
        ~~~~~~~~~~~~
        
        You must install Sequana first::
        
            pip install sequana
        
        Then, just install this package::
        
            pip install sequana_fastqc
        
        Usage
        ~~~~~
        
        ::
        
            sequana_pipelines_fastqc --help
            sequana_pipelines_fastqc --input-directory DATAPATH
        
        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.
        
        
        Tutorial
        ~~~~~~~~
        
        You can retrieve test data from sequana_fastqc (https://github.com/sequana/sequana_fastqc) or type::
        
            wget https://raw.githubusercontent.com/sequana/sequana_fastqc/master/sequana_pipelines/fastqc/data/data_R1_001.fastq.gz
            wget https://raw.githubusercontent.com/sequana/sequana_fastqc/master/sequana_pipelines/fastqc/data/data_R2_001.fastq.gz
        
        then, prepare the pipeline::
        
            sequana_fastqc --input-directory .
            cd fastqc
            sh fastq.sh
        
            # once done, remove temporary files (snakemake and others)
            make clean
        
        Just open the HTML entry called index.html and browse the multiqc report. For
        individual reports, open the tree.html file. You will get expected images such
        as the following one:
        
        .. image:: https://github.com/sequana/sequana_fastqc/blob/master/doc/summary.png?raw=true
        
        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. 
        
        Changelog
        ~~~~~~~~~
        ========= ====================================================================
        Version   Description
        ========= ====================================================================
        0.9.10    * simplify the onsuccess section
        0.9.9     * add missing png and pipeline (regression bug)
        0.9.8     * add missing multi_config file
        0.9.7     * check existence of input directory in main.py
                  * add a logo 
                  * fix schema
                  * add multiqc_config
                  * add sequana + sequana_fastqc version
        0.9.6     add the readtag option
        ========= ====================================================================
        
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
