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https://joss.theoj.org/papers/10.21105/joss.00352\n    :alt: JOSS (journal of open source software) DOI\n\n.. image:: https://github.com/sequana/trf/actions/workflows/main.yml/badge.svg?branch=main\n   :target: https://github.com/sequana/trf/actions/workflows/main.yml\n\n.. image:: https://github.com/sequana/trf/actions/workflows/apptainer.yml/badge.svg?branch=main\n   :target: https://github.com/sequana/trf/actions/workflows/apptainer.yml\n\n.. image:: https://img.shields.io/badge/python-3.11%20%7C%203.12-blue.svg\n    :target: https://pypi.python.org/pypi/sequana_trf\n    :alt: Python 3.11 | 3.12\n\nThis is the **trf** (tandem repeat finder) pipeline from the `Sequana \u003chttps://sequana.readthedocs.org\u003e`_ project\n\n:Overview: run TRF on several large datasets\n:Input: a set of FastA files\n:Output: TRF output + images\n:Status: draft\n: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\n\n\nInstallation\n~~~~~~~~~~~~\n\nIf you already have all requirements, you can install the packages using pip::\n\n    pip install sequana_trf --upgrade\n\nOtherwise, you can create a *sequana_trf* conda environment executing::\n\n    conda env create -f environment.yml\n\nand later activate the environment::\n\n  conda activate sequana_trf\n\nA third option is to install the pipeline with pip method (see above) and use singularity as explained afterwards.\n\n\nUsage\n~~~~~\n\n::\n\n    sequana_trf --help\n    sequana_trf --input-directory DATAPATH\n\nThis creates a directory with the pipeline and configuration file. You will then need\nto execute the pipeline::\n\n    cd trf\n    sh trf.sh  # for a local run\n\nThis launch a snakemake pipeline. If you are familiar with snakemake, you can\nretrieve the pipeline itself and its configuration files and then execute the pipeline yourself with specific parameters::\n\n    snakemake -s trf.rules -c config.yaml --cores 4 --stats stats.txt\n\nOr use `sequanix \u003chttps://sequana.readthedocs.io/en/main/sequanix.html\u003e`_ interface.\n\nRequirements\n~~~~~~~~~~~~\n\nThis pipeline requires the following executable(s):\n\n- trf\n\n.. image:: https://raw.githubusercontent.com/sequana/trf/main/sequana_pipelines/trf/dag.png\n\n\nDetails\n~~~~~~~~~\n\nThis pipeline runs **trf** in parallel on the input fastq files (paired or not).\nA brief sequana summary report is also produced.\n\n\nRules and configuration details\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\nHere is the `latest documented configuration file \u003chttps://raw.githubusercontent.com/sequana/trf/main/sequana_pipelines/trf/config.yaml\u003e`_\nto be used with the pipeline. Each rule used in the pipeline may have a section in the configuration file.\n\nChangelog\n~~~~~~~~~\n\n========= ====================================================================\nVersion   Description\n========= ====================================================================\n1.0.0     * Uses click and pyproject\n0.10.0    * update and add singularity containers\n0.9.3     * Use new sequana / sequana_pipetools API\n0.9.2     * Better split function of input fasta file\n0.9.0     **First release.**\n========= ====================================================================\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsequana%2Ftrf","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsequana%2Ftrf","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsequana%2Ftrf/lists"}