{"id":18448822,"url":"https://github.com/sequana/revcomp","last_synced_at":"2025-08-18T15:03:08.150Z","repository":{"id":115174974,"uuid":"227429714","full_name":"sequana/revcomp","owner":"sequana","description":"A simple utility to convert a bunch of input fastq files into their reverse complement","archived":false,"fork":false,"pushed_at":"2024-04-03T16:03:04.000Z","size":773,"stargazers_count":0,"open_issues_count":5,"forks_count":1,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-08-18T15:01:59.660Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/sequana.png","metadata":{"files":{"readme":"README.rst","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2019-12-11T18:07:24.000Z","updated_at":"2022-08-30T20:46:11.000Z","dependencies_parsed_at":"2023-12-19T19:29:36.166Z","dependency_job_id":"acd1a75f-da2a-4f39-a280-9af61827ac0f","html_url":"https://github.com/sequana/revcomp","commit_stats":{"total_commits":18,"total_committers":1,"mean_commits":18.0,"dds":0.0,"last_synced_commit":"db5255a9fe20c42a0e130a57e4aca30bf11df682"},"previous_names":[],"tags_count":3,"template":false,"template_full_name":null,"purl":"pkg:github/sequana/revcomp","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sequana%2Frevcomp","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sequana%2Frevcomp/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sequana%2Frevcomp/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sequana%2Frevcomp/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/sequana","download_url":"https://codeload.github.com/sequana/revcomp/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sequana%2Frevcomp/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":271011735,"owners_count":24684396,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-08-18T02:00:08.743Z","response_time":89,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-11-06T07:17:23.504Z","updated_at":"2025-08-18T15:03:08.069Z","avatar_url":"https://github.com/sequana.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"\n.. image:: https://badge.fury.io/py/sequana-revcomp.svg\n     :target: https://pypi.python.org/pypi/sequana_revcomp\n\n.. image:: http://joss.theoj.org/papers/10.21105/joss.00352/status.svg\n    :target: http://joss.theoj.org/papers/10.21105/joss.00352\n    :alt: JOSS (journal of open source software) DOI\n\n.. image:: https://github.com/sequana/revcomp/actions/workflows/main.yml/badge.svg\n   :target: https://github.com/sequana/revcomp/actions/workflows\n\n\n.. image:: https://img.shields.io/badge/python-3.8%20%7C%203.9%20%7C3.10-blue.svg\n    :target: https://pypi.python.org/pypi/sequana\n    :alt: Python 3.8 | 3.9 | 3.10\n\nThis is is the **revcomp** pipeline from the `Sequana \u003chttps://sequana.readthedocs.org\u003e`_ projet\n\n:Overview: revert and complement input Fast files\n:Input: A set of FastQ files (paired or single-end) compressed or not\n:Output: A set of reverse completed files\n:Status: production\n: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\n\n\n\n\nInstallation\n~~~~~~~~~~~~\n\nIf you already have all requirements, you can install the packages using pip::\n\n    pip install sequana_revcomp --upgrade\n\nUsage\n~~~~~\n\nThis command will scan all files ending in .fastq.gz found in the local\ndirectory, create a directory called revcomp where a snakemake pipeline can be executed.::\n\n::\n\n    sequana_revcomp --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 revcomp\n    sh revcomp.sh  # for a local run\n    make clean\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 revcomp.rules -c config.yaml --cores 4 \\\n        --wrapper-prefix https://raw.githubusercontent.com/sequana/sequana-wrappers/\n\nOr use `sequanix \u003chttps://sequana.readthedocs.io/en/main/sequanix.html\u003e`_ interface.\n\nRequirements\n~~~~~~~~~~~~\n\nThis pipelines requires the following executable(s):\n\n- seqtk\n\n\nDetails\n~~~~~~~~~\n\nThis pipeline runs **seqtk** in parallel on the input fastq files.\n\n\nRules and configuration details\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\nHere is the `latest documented configuration file \u003chttps://raw.githubusercontent.com/sequana/sequana_revcomp/main/sequana_pipelines/revcomp/config.yaml\u003e`_\nto be used with the pipeline. Each rule used in the pipeline may have a section in the configuration file.\n\n\nChangelog\n~~~~~~~~~\n\n========= ======================================================================\nVersion   Description\n========= ======================================================================\n0.9.0     * set singularity container\n0.8.4     * implemented --from-project option\n0.8.3     * Uses new sequana framework to spee up --help calls\n          * --threads option\n0.8.2     Fix schema and rule. output files are now saved in the ./rc directory\n0.8.1     Improve the --help message\n0.8.0     First version from sequana 0.8.0\n========= ======================================================================\n\n\nContribute \u0026 Code of Conduct\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\nTo contribute to this project, please take a look at the\n`Contributing Guidelines \u003chttps://github.com/sequana/sequana/blob/main/CONTRIBUTING.rst\u003e`_ first. Please note that this project is released with a\n`Code of Conduct \u003chttps://github.com/sequana/sequana/blob/main/CONDUCT.md\u003e`_. By contributing to this project, you agree to abide by its terms.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsequana%2Frevcomp","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsequana%2Frevcomp","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsequana%2Frevcomp/lists"}