{"id":49700641,"url":"https://github.com/fulcrumgenomics/nf-itdepends","last_synced_at":"2026-05-08T07:12:35.148Z","repository":{"id":337890552,"uuid":"1155097221","full_name":"fulcrumgenomics/nf-itdepends","owner":"fulcrumgenomics","description":" A Nextflow plugin that restores @Grab (Groovy Grape) dependency resolution for lib/ classes","archived":false,"fork":false,"pushed_at":"2026-04-29T23:09:05.000Z","size":69,"stargazers_count":5,"open_issues_count":0,"forks_count":0,"subscribers_count":0,"default_branch":"main","last_synced_at":"2026-04-30T01:10:42.058Z","etag":null,"topics":["bioinformatics","grape","groovy","ivy","nextflow","nextflow-plugin"],"latest_commit_sha":null,"homepage":"","language":"Groovy","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/fulcrumgenomics.png","metadata":{"files":{"readme":"README.md","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,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2026-02-11T05:45:03.000Z","updated_at":"2026-04-29T23:08:51.000Z","dependencies_parsed_at":null,"dependency_job_id":"5d3ecbec-3247-4b94-8cfc-95ae82af4cff","html_url":"https://github.com/fulcrumgenomics/nf-itdepends","commit_stats":null,"previous_names":["fulcrumgenomics/nf-itdepends"],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/fulcrumgenomics/nf-itdepends","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fulcrumgenomics%2Fnf-itdepends","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fulcrumgenomics%2Fnf-itdepends/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fulcrumgenomics%2Fnf-itdepends/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fulcrumgenomics%2Fnf-itdepends/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/fulcrumgenomics","download_url":"https://codeload.github.com/fulcrumgenomics/nf-itdepends/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fulcrumgenomics%2Fnf-itdepends/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":32770621,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-08T02:36:36.067Z","status":"ssl_error","status_checked_at":"2026-05-08T02:36:07.210Z","response_time":54,"last_error":"SSL_read: 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":["bioinformatics","grape","groovy","ivy","nextflow","nextflow-plugin"],"created_at":"2026-05-08T07:12:33.908Z","updated_at":"2026-05-08T07:12:35.129Z","avatar_url":"https://github.com/fulcrumgenomics.png","language":"Groovy","funding_links":[],"categories":[],"sub_categories":[],"readme":"# nf-itdepends\n\n[![Nextflow Registry](https://img.shields.io/badge/Nextflow_Registry-nf--itdepends-blue?logo=nextflow)](https://registry.nextflow.io/plugins/nf-itdepends)\n\nA Nextflow plugin that restores `@Grab` (Groovy Grape) dependency resolution for Groovy classes in the `lib/` directory.\n\n## Summary\n\nStarting with Nextflow 24.04.7-edge, [Apache Ivy was removed](https://github.com/nextflow-io/nextflow/issues/5234) from the Nextflow distribution. This broke the `@Grab` annotation, which relies on Ivy to resolve and download Maven dependencies at compile time.\n\nThis plugin brings `@Grab` back by bundling Ivy and injecting a working `GrapeEngine` into Groovy's `Grape` singleton before `lib/` files are compiled.\n\n## Get Started\n\n### Installation\n\nAdd the plugin to your `nextflow.config`:\n\n```groovy\nplugins {\n    id 'nf-itdepends@VERSION'\n}\n```\n\nReplace `VERSION` with the [latest release](https://github.com/fulcrumgenomics/nf-itdepends/releases).\n\n### Requirements\n\n- Nextflow 24.04.0 or later\n- Java 17 or later\n\n### Configuration\n\nBy default, the plugin resolves dependencies from Maven Central. Additional resolvers can be configured using `@GrabResolver` in your Groovy code:\n\n```groovy\n@GrabResolver(name='sonatype', root='https://oss.sonatype.org/content/repositories/releases/')\n@Grab('some.group:some-artifact:1.0')\nimport some.group.SomeClass\n```\n\nDependencies are cached in `~/.groovy/grapes/` (the standard Grape cache directory).\n\n## Examples\n\nUse `@Grab` in your `lib/` Groovy files as before:\n\n```groovy\n// lib/MyHelper.groovy\n@Grab('commons-lang:commons-lang:2.6')\nimport org.apache.commons.lang.StringUtils\n\nclass MyHelper {\n    static String capitalize(String input) {\n        return StringUtils.capitalize(input)\n    }\n}\n```\n\n```groovy\n// main.nf\nprocess EXAMPLE {\n    output: stdout\n    script:\n    \"\"\"\n    echo \"${MyHelper.capitalize('hello world')}\"\n    \"\"\"\n}\n\nworkflow {\n    EXAMPLE() | view\n}\n```\n\n## How It Works\n\nThe plugin exploits a timing window in the Nextflow session lifecycle:\n\n1. `Session.init()` creates `TraceObserverFactory` instances, calling `ItDependsFactory.create(session)`\n2. The factory creates an `ItDependsGrapeEngine` — a full `GrapeEngine` implementation backed by Apache Ivy, loaded from the plugin's own classloader (which bundles Ivy as a dependency)\n3. It sets `Grape.instance` to this engine via reflection\n4. Later, when `ScriptLoader.parse()` compiles `lib/` Groovy files, `@Grab` annotations fire and call our engine\n5. Our engine resolves dependencies from Maven Central, downloads JARs to `~/.groovy/grapes`, and adds them to the `GroovyClassLoader`\n\n## Development\n\n```bash\n# Build the plugin\nmake assemble\n\n# Run tests\nmake test\n\n# Install locally for testing\nmake install\n\n# Clean build artifacts\nmake clean\n```\n\n## License\n\n[MIT](LICENSE)\n\nCopyright (c) 2026 Fulcrum Genomics LLC\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffulcrumgenomics%2Fnf-itdepends","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ffulcrumgenomics%2Fnf-itdepends","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffulcrumgenomics%2Fnf-itdepends/lists"}