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 |
If you already have all requirements, you can install the packages using pip:
pip install sequana_revcomp --upgrade
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.
This pipelines requires the following executable(s):
- seqtk
This pipeline runs seqtk in parallel on the input fastq files.
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.
| Version | Description |
|---|---|
| 0.9.0 |
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| 0.8.4 |
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| 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 |
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.