{"id":18565641,"url":"https://github.com/quiltdata/nf-quilt","last_synced_at":"2025-04-10T04:33:00.575Z","repository":{"id":80201038,"uuid":"551131329","full_name":"quiltdata/nf-quilt","owner":"quiltdata","description":null,"archived":false,"fork":false,"pushed_at":"2025-03-23T22:25:58.000Z","size":1251,"stargazers_count":9,"open_issues_count":18,"forks_count":1,"subscribers_count":3,"default_branch":"main","last_synced_at":"2025-03-23T23:26:48.409Z","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":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/quiltdata.png","metadata":{"files":{"readme":"README-DEV.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}},"created_at":"2022-10-13T22:22:03.000Z","updated_at":"2024-12-25T14:29:27.000Z","dependencies_parsed_at":"2024-01-10T23:46:59.117Z","dependency_job_id":"510795f6-b69c-41ba-b8bc-ceb8d6fc37c8","html_url":"https://github.com/quiltdata/nf-quilt","commit_stats":null,"previous_names":[],"tags_count":45,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/quiltdata%2Fnf-quilt","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/quiltdata%2Fnf-quilt/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/quiltdata%2Fnf-quilt/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/quiltdata%2Fnf-quilt/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/quiltdata","download_url":"https://codeload.github.com/quiltdata/nf-quilt/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248157683,"owners_count":21057054,"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","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":"2024-11-06T22:19:37.210Z","updated_at":"2025-04-10T04:33:00.554Z","avatar_url":"https://github.com/quiltdata.png","language":"Groovy","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Developer Documentation\n\n## Using Pre-Release Versions\n\nOccasionally we will release beta versions of the plugin that are not yet\navailable in the Nextflow plugin registry. You can help test these versions as\nfollows:\n\n- Set the `NXF_PLUGINS_TEST_REPOSITORY` environment variable to the URL of the\n  plugin's metadata file\n- Specify the plugin version in the `plugins` section of your `nextflow.config`\n  file\n\nFrom the command-line, do, e.g.:\n\n```bash\nexport LOG4J_DEBUG=true  # for verbose logging\nexport VERSION=0.9.1\nexport NXF_PLUGINS_TEST_REPOSITORY=https://github.com/quiltdata/nf-quilt/releases/download/$(VERSION)/nf-quilt-$(VERSION)-meta.json\nnextflow run main.nf -plugins nf-quilt@$(VERSION)\n```\n\nFor Tower, you set the environment variables in the \"Pre-run script\".\n\n![Example Tower Pre-run Script](./images/tower-beta.png)\n\n## Using Development Versions\n\nIf you want to use edge versions of nf-quilt, you must run it with a development\nversion of `nextflow`. The simplest way to do that is to pull them both directly\nfrom GitHub:\n\n```bash\ngit clone https://github.com/nextflow.io/nextflow.git\ngit clone https://github.com/quiltdata/nf-quilt.git\ncd ./nf-quilt\n```\n\n### Verifying Nextflow\n\nIf this is your first time using Nextflow, you may also need to install a recent\n[version of Java](https://www.java.com/en/download/help/download_options.html)\nfor your platform. Nextflow itself will take care of all the other dependencies.\n\nYou can verify and compile Nextflow with:\n\n```bash\nmake nextflow\n```\n\n## Running from Git\n\nTo quickly run `nf-quilt` from this GitHub repository:\n\n```bash\n# install and compiles dependencies, then test\nmake test-all \n# create \"test/hurdat\" package on s3://$WRITE_BUCKET\nmake pkg-test WRITE_BUCKET=your-writeablebucket\n```\n\nThis ensures you have properly installed Nextflow and configured your local\n\u003c--markdownlint-disable-next-line MD041--\u003e\n[AWS credentials](https://docs.aws.amazon.com/cli/latest/userguide/cli-configure-files.html).\n\nYou can also set WRITE_BUCKET and other parameters in a `.env` file in the\nproject root, and they will be automatically read by the Makefile.\n\n### Running a Pipeline Locally\n\nFrom inside the `nf-quilt` directory, call `./launch.sh` with a path to your\npipeline.\n\nFor example, with a standard `nf-core` pipeline like `sarek`:\n\n```bash\n./launch.sh run nf-core/sarek -profile test,docker -plugins nf-quilt --outdir \"quilt+s3://bucket#package=nf-quilt/sarek\"\n```\n\nOtherwise, replace `nf-core/sarek` with the local path to your pipeline's `.nf`\nfile (be sure to rename the `outdir` parameter if you use different convention).\nFor example:\n\n```bash\n./launch.sh run ./main.nf -profile standard -plugins $(PROJECT) --outdir \"quilt+s3://bucket#package=test/hurdat\"\n```\n\nThere are standard Makefile targets for both `sarek` and `fetchngs` pipelines, which will test against the latest published versions of nf-quilt:\n\n```bash\nmake sarek\nmake fetchngs\n```\n\n### Unit Testing\n\nYou can cleanly compile and run all unit tests with:\n\n```bash\nmake check\n```\n\nTo show the output of the tests, use:\n\n```bash\nmake verify\n```\n\nTo fast-fail on the first failing test, use:\n\n```bash\nmake fast\n```\n\n## Publishing the Plugin for Others to Use\n\nIf your system is properly configured, use `make publish` to package, upload,\nand publish the plugin.\n\nOtherwise, follow these steps:\n\n1. Create a file named `gradle.properties` in the user's home (NOT project)\n   directory containing the following attributes:\n\n   - `github_organization`: the GitHub organisation where the plugin repository\n     is hosted.\n   - `github_username`: The GitHub username granting access to the plugin\n     repository.\n   - `github_access_token`: The GitHub access token required to upload and\n     commit changes to the plugin repository.\n   - `github_commit_email`: The email address associated with your GitHub\n     account.\n\n2. Use the following command to package and create a release for your plugin on\n   GitHub:\n\n   ```bash\n   ./gradlew :plugins:nf-quilt:upload\n   ```\n\n3. Fork the [nextflow-io/plugins](https://github.com/nextflow-io/plugins)\n   repository to one you can write to\n\n4. Use the following command to publish your plugin to your fork:\n\n   ```bash\n   ./gradlew :plugins:publishIndex\n   ```\n\n5. Create a pull request to push your changes back to\n   [nextflow-io/plugins](https://github.com/nextflow-io/plugins/blob/main/plugins.json)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fquiltdata%2Fnf-quilt","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fquiltdata%2Fnf-quilt","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fquiltdata%2Fnf-quilt/lists"}