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 bash revcomp.sh # for a local run
This launches a snakemake pipeline.
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 |
|---|---|
1.2.0 |
|
1.1.0 |
|
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 |
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.
1 maintainer
Metadata
1 maintainer
Release files for sequana-revcomp 1.2.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| sequana_revcomp-1.2.0.tar.gz | 5.0 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| sequana_revcomp-1.2.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 12.1 kB
Release files / sequana_revcomp-1.2.0.tar.gz
| Download URL | sequana_revcomp-1.2.0.tar.gz |
|---|---|
| Size | 5.0 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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| Upload date | |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.1.0 CPython/3.13.12
|
Release files / sequana_revcomp-1.2.0-py3-none-any.whl
| Download URL | sequana_revcomp-1.2.0-py3-none-any.whl |
|---|---|
| Size | 7.0 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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| Upload date | |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.1.0 CPython/3.13.12
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