sequana-rnaseq 0.8.1

A fastqc pipeline from sequana project.

This is is the rnaseq pipeline from the Sequana projet

Overview:

TODO

Input:

TODO

Output:

TODO

Status:

draft

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 --run-mode local
sequana_pipelines_rnaseq --input-directory DATAPATH --run-mode slurm

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 interface.

Requirements

This pipelines requires the following executable(s):

• TODO

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 to be used with the pipeline. Each rule used in the pipeline may have a section in the configuration file.