https://github.com/sequana/revcomp
A simple utility to convert a bunch of input fastq files into their reverse complement
https://github.com/sequana/revcomp
Last synced: 10 months ago
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A simple utility to convert a bunch of input fastq files into their reverse complement
- Host: GitHub
- URL: https://github.com/sequana/revcomp
- Owner: sequana
- License: bsd-3-clause
- Created: 2019-12-11T18:07:24.000Z (over 6 years ago)
- Default Branch: main
- Last Pushed: 2024-04-03T16:03:04.000Z (about 2 years ago)
- Last Synced: 2025-08-18T15:01:59.660Z (10 months ago)
- Language: Python
- Size: 755 KB
- Stars: 0
- Watchers: 2
- Forks: 1
- Open Issues: 5
-
Metadata Files:
- Readme: README.rst
- License: LICENSE
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README
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.. image:: http://joss.theoj.org/papers/10.21105/joss.00352/status.svg
:target: http://joss.theoj.org/papers/10.21105/joss.00352
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:alt: Python 3.8 | 3.9 | 3.10
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.