{"id":25905384,"url":"https://github.com/stevekm/nf-niceutils","last_synced_at":"2026-05-11T10:35:42.017Z","repository":{"id":229064624,"uuid":"775036751","full_name":"stevekm/nf-niceutils","owner":"stevekm","description":"nice utility methods for Nextflow pipelines","archived":false,"fork":false,"pushed_at":"2024-05-09T01:26:12.000Z","size":416,"stargazers_count":0,"open_issues_count":6,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2024-05-21T16:57:07.926Z","etag":null,"topics":["multiqc","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/stevekm.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","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":"2024-03-20T16:39:58.000Z","updated_at":"2024-05-21T14:43:17.000Z","dependencies_parsed_at":"2024-05-21T17:04:04.174Z","dependency_job_id":null,"html_url":"https://github.com/stevekm/nf-niceutils","commit_stats":null,"previous_names":["stevekm/nf-niceutils"],"tags_count":2,"template":false,"template_full_name":"edn-es/nf-plugin-template","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stevekm%2Fnf-niceutils","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stevekm%2Fnf-niceutils/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stevekm%2Fnf-niceutils/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stevekm%2Fnf-niceutils/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/stevekm","download_url":"https://codeload.github.com/stevekm/nf-niceutils/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":241610990,"owners_count":19990508,"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":["multiqc","nextflow","nextflow-plugin"],"created_at":"2025-03-03T05:15:00.152Z","updated_at":"2026-05-11T10:35:41.963Z","avatar_url":"https://github.com/stevekm.png","language":"Groovy","funding_links":[],"categories":[],"sub_categories":[],"readme":"# `nf-niceutils`\n\nA set of nice utility methods for use with Nextflow pipelines\n\n## Under Construction\n\nThis plugin is currently under construction. Please see the details in `NOTES.md` for development and usage. And check out `examples/test.nf` to see how the plugin is used in a Nextflow pipeline.\n\n## Usage\n\nAn example workflow is included so you can see how the plugin can be used.\n\nRun the basic workflow with\n\n```bash\nnextflow run examples/test.nf\n```\n\nYou will get the following files\n\n- `output/software_versions_mqc.yaml` : a software versions table for use with MultiQC\n- `output/workflow_summary_mqc.yaml` : a workflow summary table for use with MultiQC\n\nIf you have Docker running you can run the full example\n\n```bash\nnextflow run examples/test.nf -profile multiqc\n```\n\nThis will also give you the following file\n\n- `output/multiqc_report.html` : a MultiQC report that utilizes the created tables\n\nSome examples of the output are included in the repo here at `examples/example_output`.\n\n### Usage with your own pipelines\n\nTo use it with your own pipeline, currently you will need to make sure to include it in your `nextflow.config`;\n\n```groovy\nplugins {\n    id 'nf-niceutils'\n}\n```\n\nand run it like this\n\n```bash\nNXF_PLUGINS_TEST_REPOSITORY=https://raw.githubusercontent.com/stevekm/nextflow-plugins-registry/main/plugins.json nextflow run main.nf\n```\n\nSome time soon hopefully I can get it pushed into the official Nextflow registry :)\n\n## Methods\n\n(these are subject to change)\n\nThe following methods are the most useful ones offered by the plugin;\n\n- `createProcessVersionFromYAMLstrList` : creates a MultiQC Software Versions Table YAML with embedded HTML table\n- `workflowSummaryTableStr`: creates a workflow summary table YAML for use with MultiQC\n\nYou can see examples of how to use each function inside the `examples/test.nf` script.\n\n### `createProcessVersionFromYAMLstrList`\n\n```groovy\n    // create a MultiQC Software Versions Table YAML + HTML\n    // versions_ch contains versions.yml files output by Nextflow processes\n    mqc_versions_ch = versions_ch.map{ it.text }\n        .collect()\n        .map{ versions -\u003e\n            def processList = createProcessVersionFromYAMLstrList(versions)\n            makeVersionsYAML(\n                processList,\n                workflow.manifest.name,\n                workflow.manifest.homePage,\n                workflow.manifest.version,\n                workflow.nextflow.version.toString()\n                )\n        }.collectFile(storeDir: \"${params.outdir}\", name: \"software_versions_mqc.yaml\")\n```\n\n### `workflowSummaryTableStr`\n\n```groovy\n    // create a workflow summary table\n    workflow_summary_ch = Channel.from(\n        workflowSummaryTableStr(\n            params,\n            workflow.properties,\n            workflow.manifest.properties,\n            ['foo_key'] // some 'bad params' to exclude from the output\n            )\n    ).collectFile(storeDir: \"${params.outdir}\", name: \"workflow_summary_mqc.yaml\")\n```","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fstevekm%2Fnf-niceutils","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fstevekm%2Fnf-niceutils","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fstevekm%2Fnf-niceutils/lists"}