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 doi:10.21105/joss.00352
Installation
If you already have all requirements, you can install the packages using pip:
pip install sequana_mapper --upgrade
Usage
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 |
|
0.8.4 |
|
0.8.3 |
|
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 |
1 maintainer
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Source Distribution
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