sequana-ribofinder 0.10.1

NGS, ribosomal, rRNA, snakemake, sequana

This is is the ribofinder pipeline from the Sequana project

Overview:

Simple parallele workflow to detect and report ribosomal content

Input:

FastQ files

Output:

HTML reports

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 (use –upgrade to get the latest version installed):

pip install sequana --upgrade

Then, just install this package:

pip install sequana_ribofinder --upgrade

Usage

This command will scan all files ending in .fastq.gz found in the local directory, create a directory called fastqc/ where a snakemake pipeline is launched automatically. Depending on the number of files and their sizes, the process may be long:

sequana_pipelines_ribofinder --help
sequana_pipelines_ribofinder --input-directory DATAPATH

This creates a directory with the pipeline and configuration file. You will then need to execute the pipeline:

cd ribofinder
sh ribofinder.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 ribofinder.rules -c config.yaml --cores 4 --stats stats.txt

Or use sequanix interface.

Requirements

This pipelines requires the following executable(s):

• bowtie1

Details

This pipeline runs ribofinder in parallel on the input fastq files. 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.

Changelog

Version	Description
0.10.1	add additional test and fix bug in pipeline (regression bug)
0.10.0	Update to use sequana-wrappers. Remove multiqc. summary.html is self-content
0.9.3	fix logger
0.9.2	First release.