Metadata-Version: 1.2
Name: sequana_demultiplex
Version: 0.9.7
Summary: Pipeline that runs bcl2fastq and creates additional plots within a Snakemake workflow
Home-page: https://github.com/sequana/
Author: cokelaer
Author-email: thomas.cokelaer@pasteur.fr
Maintainer: cokelaer
Maintainer-email: thomas.cokelaer@pasteur.fr
License: new BSD
Description: This is is the **demultiplex** pipeline from the `Sequana <https://sequana.readthedocs.org>`_ projet
        
        :Overview: Runs bcl2fastq on raw BCL data and creates plots to ease the QC validation
        :Input: A valid Illumina base calling directory
        :Output: a set of PNG files and the expected FastQ files
        :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_demultiplex
        
        Usage
        ~~~~~
        
        ::
        
            sequana_pipelines_demultiplex --help
            sequana_pipelines_demultiplex --working-directory DATAPATH --bcl-directory bcldata
        
        This creates a directory **fastq**. You just need to execute the pipeline::
        
            cd demutliplex
            sh demutliplex.sh  # for a local run
        
        This launch a snakemake pipeline. If you are familiar with snakemake, you can retrieve the demutliplex.rules and config.yaml files and then execute the pipeline yourself with specific parameters::
        
            snakemake -s demutliplex.rules --cores 4 --stats stats.txt
        
        Or use `sequanix <https://sequana.readthedocs.io/en/master/sequanix.html>`_ interface.
        
        Would you need to merge the lane, please add the --merging-strategy argument
        followed by *merge*::
        
            sequana_pipelines_demultiplex --bcl-directory bcl_data --merging-strategy merge
           
        
        Requirements
        ~~~~~~~~~~~~
        
        This pipelines requires the following executable(s):
        
        - bcl2fastq 2.20.0
        
        
        .. image:: https://raw.githubusercontent.com/sequana/sequana_demultiplex/master/sequana_pipelines/demultiplex/dag.png
        
        
        Details
        ~~~~~~~~~
        
        This pipeline runs bcl2fastq 2.20 and creates a set of diagnostics plots to help
        deciphering common issues such as missing index and sample sheet errors. 
        
        
        
        Rules and configuration details
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        Here is the `latest documented configuration file <https://raw.githubusercontent.com/sequana/sequana_demutliplex/master/sequana_pipelines/demutliplex/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
        ========= ====================================================================
        0.9.7     * Use new release of sequana_pipetools
                  * set matplotlib backend to agg
                  * include a simple HTML report
        0.9.6     * Handle different RunParameter.xml name (NextSeq vs HiSeq)
        0.9.5     * Fix a regression bug due to new sequana release. We do not check 
                    the input file (fastq) since this is not a sequence analysis
                    pipeline
                  * Check whether it is a NextSeq run. If so, merging-strategy must be
                    set to 'merge'. Can be bypassed using --force
        0.9.4     * Check the presence of the bcl input directory and samplesheet. 
                  * More help in the --help message. 
                  * add  --sample-sheet option to replace --samplesheet option
                  * Fix the schema file
                  * Check for presence of RunParameters.xml and provide information
                    if merging-stratgy is set to None whereas it is a NextSeq run
        0.9.3     Fix regression bug
        0.9.2     remove warning due to relative paths. 
        0.9.1     Make the merging options compulsory. Users must tell whether they 
                  want to merge the lanes or not. This avoid to do the merging or not 
                  whereas the inverse was expected.
        0.8.6     Uses 64G/biomics queue and 16 cores on a SLURM scheduler
        ========= ====================================================================
        
        
Keywords: bcl2fastq, Illumina, bcl, fastq, demultiplexing, base caller,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 :: 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
