https://github.com/sequana/trf
parallell version of trf
https://github.com/sequana/trf
Last synced: about 2 months ago
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parallell version of trf
- Host: GitHub
- URL: https://github.com/sequana/trf
- Owner: sequana
- License: bsd-3-clause
- Created: 2020-09-14T17:12:49.000Z (over 5 years ago)
- Default Branch: main
- Last Pushed: 2026-04-04T18:57:58.000Z (2 months ago)
- Last Synced: 2026-04-04T19:21:24.428Z (2 months ago)
- Language: Python
- Size: 204 KB
- Stars: 0
- Watchers: 1
- Forks: 1
- Open Issues: 1
-
Metadata Files:
- Readme: README.rst
- License: LICENSE
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README
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This is the **trf** (tandem repeat finder) pipeline from the `Sequana `_ project
:Overview: run TRF on several large datasets
:Input: a set of FastA files
:Output: TRF output + images
:Status: draft
: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_trf --upgrade
Otherwise, you can create a *sequana_trf* conda environment executing::
conda env create -f environment.yml
and later activate the environment::
conda activate sequana_trf
A third option is to install the pipeline with pip method (see above) and use singularity as explained afterwards.
Usage
~~~~~
::
sequana_trf --help
sequana_trf --input-directory DATAPATH
This creates a directory with the pipeline and configuration file. You will then need
to execute the pipeline::
cd trf
sh trf.sh # for a local run
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 trf.rules -c config.yaml --cores 4 --stats stats.txt
Or use `sequanix `_ interface.
Requirements
~~~~~~~~~~~~
This pipeline requires the following executable(s):
- trf
.. image:: https://raw.githubusercontent.com/sequana/trf/main/sequana_pipelines/trf/dag.png
Details
~~~~~~~~~
This pipeline runs **trf** in parallel on the input fastq files (paired or not).
A brief sequana summary report is also produced.
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
========= ====================================================================
1.0.0 * Uses click and pyproject
0.10.0 * update and add singularity containers
0.9.3 * Use new sequana / sequana_pipetools API
0.9.2 * Better split function of input fasta file
0.9.0 **First release.**
========= ====================================================================