{"id":48232283,"url":"https://github.com/bactopia/nf-bactopia","last_synced_at":"2026-04-04T19:42:24.501Z","repository":{"id":289192170,"uuid":"968833956","full_name":"bactopia/nf-bactopia","owner":"bactopia","description":"A Nextflow plugin for Bactopia","archived":false,"fork":false,"pushed_at":"2026-03-30T01:14:34.000Z","size":430,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2026-03-30T04:53:09.602Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Groovy","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/bactopia.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":null,"funding":null,"license":"COPYING","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,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2025-04-18T20:25:56.000Z","updated_at":"2026-03-30T01:14:38.000Z","dependencies_parsed_at":null,"dependency_job_id":"1d8280e9-412e-4893-9353-87453827c3a3","html_url":"https://github.com/bactopia/nf-bactopia","commit_stats":null,"previous_names":["bactopia/nf-bactopia"],"tags_count":3,"template":false,"template_full_name":null,"purl":"pkg:github/bactopia/nf-bactopia","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bactopia%2Fnf-bactopia","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bactopia%2Fnf-bactopia/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bactopia%2Fnf-bactopia/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bactopia%2Fnf-bactopia/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/bactopia","download_url":"https://codeload.github.com/bactopia/nf-bactopia/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bactopia%2Fnf-bactopia/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":31411350,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-04-04T19:29:44.979Z","status":"ssl_error","status_checked_at":"2026-04-04T19:29:11.535Z","response_time":60,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":"2026-04-04T19:42:24.044Z","updated_at":"2026-04-04T19:42:24.480Z","avatar_url":"https://github.com/bactopia.png","language":"Groovy","funding_links":[],"categories":[],"sub_categories":[],"readme":"# nf-bactopia\n\n[![nf-bactopia CI](https://github.com/bactopia/nf-bactopia/workflows/nf-bactopia%20CI/badge.svg)](https://github.com/bactopia/nf-bactopia/actions)\n[![codecov](https://codecov.io/gh/bactopia/nf-bactopia/branch/main/graph/badge.svg)](https://codecov.io/gh/bactopia/nf-bactopia)\n[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)\n\nA Nextflow plugin for specifically for usage with [Bactopia](https://bactopia.github.io/). It\nbased of the modified [nf-core libs](https://github.com/bactopia/bactopia/tree/4b075af96da522222bb075d4b65927d1ba3de9c2/lib)\nand the [nf-schema plugin](https://github.com/nextflow-io/nf-schema).\n\nThis plugin will replicate the functionality of the previous libraries, while being compatible\nwith future releases of Nextflow (\u003e= 25).\n\nAgain, while you are free to do what you want, this plugin is specifically designed for Bactopia\nand will likely not work with other pipelines.\n\n## Setting up a Development Environment\n\n### Clone the repository\n\n```{bash}\ngit clone git@github.com:bactopia/nf-bactopia.git\n\ncd nf-bactopia\n```\n\n### Create a new conda environment\n\n```{bash}\nconda create -y -n nf-bactopia \\\n    -c conda-forge \\\n    -c bioconda \\\n    make \\\n    'nextflow\u003e=25'\nconda activate nf-bactopia\n```\n\n### Build the plugin and install\n\n```{bash}\nmake assemble\nmake install\n```\n\n### Use the plugin\n\nThe `make install` should put the plugin in your `~/.nextflow/plugins` directory. So it should\njust work!\n\n```{bash}\nNXF_VER=25.06.0-edge nextflow run ...\n```\n\n## Testing\n\nThis plugin has comprehensive test coverage with 230 unit tests covering 61.6% of the codebase.\n\n### Run tests\n\n```bash\n# Run all unit tests\n./gradlew test\n\n# Run tests with coverage report\n./gradlew test jacocoTestReport\n\n# View coverage report\nopen build/reports/jacoco/test/html/index.html\n```\n\n### Coverage metrics\n\n- **Instruction Coverage**: 61.6% (11,636 / 18,884 instructions)\n- **Method Coverage**: 65.4%\n- **Class Coverage**: 70.0%\n- **Total Tests**: 230 (all passing ✓)\n\nSee [docs/TESTING.md](docs/TESTING.md) for detailed testing documentation.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbactopia%2Fnf-bactopia","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbactopia%2Fnf-bactopia","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbactopia%2Fnf-bactopia/lists"}