Metadata-Version: 1.2
Name: sequana-rnaseq
Version: 0.9.16
Summary: A RNAseq pipeline from raw reads to feature counts
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 **rnaseq** pipeline from the `Sequana <https://sequana.readthedocs.org>`_ projet
        
        :Overview: RNASeq analysis from raw data to feature counts
        :Input: A set of Fastq Files and genome reference and annotation.
        :Output: MultiQC reports and feature Counts
        :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
        ~~~~~~~~~~~~
        
        You must install Sequana first::
        
            pip install sequana
        
        Then, just install this package::
        
            pip install sequana_rnaseq
        
        
        Usage
        ~~~~~
        
        ::
        
            sequana_pipelines_rnaseq --help
            sequana_pipelines_rnaseq --input-directory DATAPATH --genome-directory genome --aligner star
        
        This creates a directory with the pipeline and configuration file. You will then need 
        to execute the pipeline::
        
            cd rnaseq
            sh rnaseq.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 rnaseq.rules -c config.yaml --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):
        
        - bowtie
        - bowtie2
        - STAR
        - featureCounts (subread package)
        - picard
        - multiqc
        
        More may be needed depending on the configuration file options. For instance,
        you may use fastq_screen, in which case you need to install it and configure it. 
        
        .. image:: https://raw.githubusercontent.com/sequana/sequana_rnaseq/master/sequana_pipelines/rnaseq/dag.png
        
        
        Details
        ~~~~~~~~~
        
        This pipeline runs **rnaseq** in parallel on the input fastq files (paired or not). 
        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_rnaseq/master/sequana_pipelines/rnaseq/config.yaml>`_
        to be used with the pipeline. Each rule used in the pipeline may have a section in the configuration file. 
        
        
        .. warning:: the RNAseQC rule is switch off and is not currently functional in
           version 0.9.X
        
        Changelog
        ~~~~~~~~~
        
        ========= ====================================================================
        Version   Description
        ========= ====================================================================
        0.9.16    * Best feature_counts is now saved into rnadiff/feature_counts 
                    directory and rnadiff scripts have been updated accordingly
                  * the most probable feature count option is now computed more
                    effectivily and incorporated inside the Snakemake pipeline (not in
                    the onsuccess) so that multiqc picks the best one (not the 3 
                    results)
                  * the target.txt file can be generated inside the pipeline if user
                    fill the rnadiff/conditions section in the config file
                  * indexing options are filled automatically when calling
                    sequana_rnaseq based on the presence/absence of the index 
                    of the aligner being used.
                  * salmon now integrated and feature counts created (still WIP in
                    sequana)
        0.9.15    * FastQC on raw data skipped by default (FastQC
                    for processed data is still available)
                  * Added paired options (-p) for featureCounts
                  * Switch back markduplicates to False for now.
        0.9.14    * Use only R1 with bowtie1
                  * set the memory requirements for mark_duplicates in cluster_config
                    file
                  * Set temporary directory for mark_duplicates to be local ./tmp
        0.9.13    * set mark_duplicate to true by default
                  * use new sequana pipeline manager
                  * export all features counts in a single file
                  * custom HTML report
                  * faster --help calls
                  * --from-project option added
        0.9.12    * include salmon tool as an alternative to star/bowtie2
                  * include rnadiff directory with required input for Differential
                    analysis
        0.9.11    * Automatic guessing of the strandness of the experiment
        0.9.10    * Fix multiqc for RNAseQC rule
        0.9.9     * Fix RNAseQC rule, which is now available. 
                  * Fix ability to use existing rRNA file as input
        0.9.8     * Fix indexing for bowtie1 to not be done if aligner is different
                  * add new options: --feature-counts-options and --do-rnaseq-qc,
                    --rRNA-feature
                  * Based on the input GFF, we now check the validity of the rRNA
                    feature and feature counts options to check whether the feature 
                    exists in the GFF
                  * schema is now used to check the config file values
                  * add a data test for testing and documentation
        0.9.7     * fix typo found in version 0.9.6
        0.9.6     * Fixed empty read tag in the configuration file
                  * Possiblity to switch off cutadapt section
                  * Fixing bowtie2 rule in sequana and update the pipeline accordingly
                  * Include a schema file
                  * output-directory parameter renamed into output_directory (multiqc 
                    section)
                  * handle stdout correctly in fastqc, bowtie1, bowtie2 rules
        0.9.5     * Fixed https://github.com/sequana/sequana/issues/571
                  * More cutadapt commands and sanity checks
                  * Fixed bowtie2 options import in rnaseq.rules
        0.9.4  
        0.9.3     if a fastq_screen.conf is provided, we switch the fastqc_screen 
                  section ON automatically
        0.9.0     **Major refactorisation.**
        
                  * remove sartools, kraken rules. 
                  * Indexing is now optional and can be set in the configuration.
                  * Configuration file is simplified  with a general section to enter
                    the genome location and aligner. 
                  * Fixed rules in  sequana (0.8.0) that were not up-to-date with
                    several executables used in the  pipeline including picard,
                    fastq_screen, etc. See Sequana Changelog for details with respect
                    to rules changes. 
                  * Copying the feature counts in main directory  ready to use for 
                    a differential analysis.
        ========= ====================================================================
        
Keywords: snakemake, sequana, RNAseq, RNADiff, differential analysis
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
