This is is the revcomp pipeline from the Sequana projet

Overview

revert and complement input Fast files

Input

A set of FastQ files (paired or single-end) compressed or not

Output

A set of reverse completed 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

If you already have all requirements, you can install the packages using pip:

pip install sequana_revcomp --upgrade

Usage

This command will scan all files ending in .fastq.gz found in the local directory, create a directory called revcomp where a snakemake pipeline can be executed.:

::

sequana_revcomp --input-directory DATAPATH

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

cd revcomp
sh revcomp.sh  # for a local run
make clean

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 revcomp.rules -c config.yaml --cores 4 \
    --wrapper-prefix https://raw.githubusercontent.com/sequana/sequana-wrappers/

Or use sequanix interface.

Requirements

This pipelines requires the following executable(s):

• seqtk

Details

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

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
0.9.0	* set singularity container
0.8.4	* implemented --from-project option
0.8.3	Uses new sequana framework to spee up --help calls --threads option
0.8.2	Fix schema and rule. output files are now saved in the ./rc directory
0.8.1	Improve the --help message
0.8.0	First version from sequana 0.8.0

Contribute & Code of Conduct

To contribute to this project, please take a look at the Contributing Guidelines first. Please note that this project is released with a Code of Conduct. By contributing to this project, you agree to abide by its terms.