sequana-revcomp 1.1.0

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

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.