sequana-revcomp 1.1.0

Description:

sequanarevcomp 1.1.0

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.