{"id":20153449,"url":"https://github.com/nextflow-io/nf-validation","last_synced_at":"2025-04-09T21:33:12.438Z","repository":{"id":54314521,"uuid":"340163040","full_name":"nextflow-io/nf-validation","owner":"nextflow-io","description":"Params validation plugin for Nextflow pipelines","archived":false,"fork":false,"pushed_at":"2024-04-22T13:36:41.000Z","size":3070,"stargazers_count":47,"open_issues_count":27,"forks_count":19,"subscribers_count":5,"default_branch":"master","last_synced_at":"2024-04-22T13:45:53.933Z","etag":null,"topics":["json-schema","nextflow","plugin","samplesheet","validation"],"latest_commit_sha":null,"homepage":"https://nextflow-io.github.io/nf-validation/","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/nextflow-io.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":"docs/contributing/setup.md","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}},"created_at":"2021-02-18T20:00:05.000Z","updated_at":"2024-04-22T13:45:59.184Z","dependencies_parsed_at":"2023-10-12T19:31:11.280Z","dependency_job_id":"bc466cce-30ed-4c18-92bd-fe07c731aaf2","html_url":"https://github.com/nextflow-io/nf-validation","commit_stats":null,"previous_names":[],"tags_count":14,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nextflow-io%2Fnf-validation","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nextflow-io%2Fnf-validation/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nextflow-io%2Fnf-validation/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nextflow-io%2Fnf-validation/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/nextflow-io","download_url":"https://codeload.github.com/nextflow-io/nf-validation/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248114962,"owners_count":21050146,"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":["json-schema","nextflow","plugin","samplesheet","validation"],"created_at":"2024-11-13T23:19:05.949Z","updated_at":"2025-04-09T21:33:12.392Z","avatar_url":"https://github.com/nextflow-io.png","language":"Groovy","readme":"# ![nf-validation](docs/images/nf-validation.svg)\n\n**A Nextflow plugin to work with validation of pipeline parameters and sample sheets.**\n\n\u003c!-- prettier-ignore --\u003e\n\u003e [!IMPORTANT]\n\u003e # `nf-validation` has now been renamed to `nf-schema`.\n\u003e **The `nf-validation` plugin will not receive any future updates.**\n\u003e **Please update your pipelines to use [`nf-schema`](https://github.com/nextflow-io/nf-schema) instead.**\n\u003e \n\u003e See \u003chttps://github.com/nextflow-io/nf-schema\u003e for details.\n\u003e\n\u003e This change was necessary to prevent older versions of `nf-core` pipelines from with unpinned plugin references from breaking when updating to the latest version of `nf-validation`.\n\u003e **Please pin the version of `nf-schema` in your pipeline's `nextflow.config` file:**\n\u003e ```nextflow\n\u003e plugins { id 'nf-schema@2.0.0' }\n\u003e ```\n\n## Introduction\n\nThis [Nextflow plugin](https://www.nextflow.io/docs/latest/plugins.html#plugins) provides a number of functions that can be included into a Nextflow pipeline script to work with parameter and sample sheet schema. Using these functions you can:\n\n- 📖 Print usage instructions to the terminal (for use with `--help`)\n- ✍️ Print log output showing parameters with non-default values\n- ✅ Validate supplied parameters against the pipeline schema\n- 📋 Validate the contents of supplied sample sheet files\n- 🛠️ Create a Nextflow channel with a parsed sample sheet\n\nSupported sample sheet formats are CSV, TSV and YAML (simple).\n\n## Quick Start\n\nDeclare the plugin in your Nextflow pipeline configuration file:\n\n```groovy title=\"nextflow.config\"\nplugins {\n  id 'nf-validation'\n}\n```\n\nThis is all that is needed - Nextflow will automatically fetch the plugin code at run time.\n\n\u003e [!NOTE]\n\u003e The snippet above will always try to install the latest version, good to make sure\n\u003e that the latest bug fixes are included! However, this can cause difficulties if running\n\u003e offline. You can pin a specific release using the syntax `nf-validation@0.3.2`\n\nYou can now include the plugin helper functions into your Nextflow pipeline:\n\n```groovy title=\"main.nf\"\ninclude { validateParameters; paramsHelp; paramsSummaryLog; fromSamplesheet } from 'plugin/nf-validation'\n\n// Print help message, supply typical command line usage for the pipeline\nif (params.help) {\n   log.info paramsHelp(\"nextflow run my_pipeline --input input_file.csv\")\n   exit 0\n}\n\n// Validate input parameters\nvalidateParameters()\n\n// Print summary of supplied parameters\nlog.info paramsSummaryLog(workflow)\n\n// Create a new channel of metadata from a sample sheet\n// NB: `input` corresponds to `params.input` and associated sample sheet schema\nch_input = Channel.fromSamplesheet(\"input\")\n```\n\n## Dependencies\n\n- Java 11 or later\n- \u003chttps://github.com/everit-org/json-schema\u003e\n\n## Slack channel\n\nThere is a dedicated [nf-validation Slack channel](https://nfcore.slack.com/archives/C056RQB10LU) in the [Nextflow Slack workspace](nextflow.slack.com).\n\n## Credits\n\nThis plugin was written based on code initially written within the nf-core community,\nas part of the nf-core pipeline template.\n\nWe would like to thank the key contributors who include (but are not limited to):\n\n- Júlia Mir Pedrol ([@mirpedrol](https://github.com/mirpedrol))\n- Nicolas Vannieuwkerke ([@nvnieuwk](https://github.com/nvnieuwk))\n- Kevin Menden ([@KevinMenden](https://github.com/KevinMenden))\n- Phil Ewels ([@ewels](https://github.com/ewels))\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnextflow-io%2Fnf-validation","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fnextflow-io%2Fnf-validation","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnextflow-io%2Fnf-validation/lists"}