{"id":13477550,"url":"https://github.com/nf-core/modules","last_synced_at":"2026-01-16T06:57:30.622Z","repository":{"id":36968357,"uuid":"198982083","full_name":"nf-core/modules","owner":"nf-core","description":"Repository to host tool-specific module files for the Nextflow DSL2 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![nf-core/modules](docs/images/nfcore-modules_logo.png)\n\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg?labelColor=000000)](https://www.nextflow.io/)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000\u0026logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000\u0026logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n\n\u003c!-- ![GitHub Actions Coda Linting](https://github.com/nf-core/modules/workflows/Code%20Linting/badge.svg) --\u003e\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23modules-4A154B?labelColor=000000\u0026logo=slack)](https://nfcore.slack.com/channels/modules)\n[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000\u0026logo=bluesky)](https://bsky.app/profile/nf-co.re)\n[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF\u0026logo=mastodon)](https://mstdn.science/@nf_core)\n[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000\u0026logo=youtube)](https://www.youtube.com/c/nf-core)\n\nA repository for hosting [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) module files containing tool-specific process definitions and their associated documentation.\n\n## Table of contents\n\n- [Using existing modules](#using-existing-modules)\n- [Adding new modules](#adding-new-modules)\n- [Help](#help)\n- [Citation](#citation)\n\n## Using existing modules\n\nThe module files hosted in this repository define a set of processes for software tools such as `fastqc`, `bwa`, `samtools` etc. This allows you to share and add common functionality across multiple pipelines in a modular fashion.\n\nWe have written a helper command in the `nf-core/tools` package that uses the GitHub API to obtain the relevant information for the module files present in the [`modules/`](modules/) directory of this repository. This includes using `git` commit hashes to track changes for reproducibility purposes, and to download and install all of the relevant module files.\n\n1. Install the latest version of [`nf-core/tools`](https://github.com/nf-core/tools#installation) (`\u003e=2.0`)\n2. List the available modules:\n\n```console\n$ nf-core modules list remote\n\n                                      ,--./,-.\n      ___     __   __   __   ___     /,-._.--~\\\n|\\ | |__  __ /  ` /  \\ |__) |__         }  {\n| \\| |       \\__, \\__/ |  \\ |___     \\`-._,-`-,\n                                      `._,._,'\n\nnf-core/tools version 2.0\n\nINFO     Modules available from nf-core/modules (master):                       pipeline_modules.py:164\n\n┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓\n┃ Module Name                    ┃\n┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩\n│ bandage/image                  │\n│ bcftools/consensus             │\n│ bcftools/filter                │\n│ bcftools/isec                  │\n..truncated..\n```\n\n3. Install the module in your pipeline directory:\n\n```console\n$ nf-core modules install fastqc\n\n                                      ,--./,-.\n      ___     __   __   __   ___     /,-._.--~\\\n|\\ | |__  __ /  ` /  \\ |__) |__         }  {\n| \\| |       \\__, \\__/ |  \\ |___     \\`-._,-`-,\n                                      `._,._,'\n\nnf-core/tools version 2.0\n\nINFO     Installing fastqc                                                      pipeline_modules.py:213\nINFO     Downloaded 3 files to ./modules/nf-core/modules/fastqc                 pipeline_modules.py:236\n```\n\n4. Import the module in your Nextflow script:\n\n```nextflow\n#!/usr/bin/env nextflow\n\nnextflow.enable.dsl = 2\n\ninclude { FASTQC } from './modules/nf-core/modules/fastqc/main'\n```\n\n5. Remove the module from the pipeline repository if required:\n\n```console\n$ nf-core modules remove fastqc\n\n                                      ,--./,-.\n      ___     __   __   __   ___     /,-._.--~\\\n|\\ | |__  __ /  ` /  \\ |__) |__         }  {\n| \\| |       \\__, \\__/ |  \\ |___     \\`-._,-`-,\n                                      `._,._,'\n\nnf-core/tools version 2.0\n\nINFO     Removing fastqc                                                        pipeline_modules.py:271\nINFO     Successfully removed fastqc                                            pipeline_modules.py:285\n```\n\n6. Check that a locally installed nf-core module is up-to-date compared to the one hosted in this repo:\n\n```console\n$ nf-core modules lint fastqc\n\n                                      ,--./,-.\n      ___     __   __   __   ___     /,-._.--~\\\n|\\ | |__  __ /  ` /  \\ |__) |__         }  {\n| \\| |       \\__, \\__/ |  \\ |___     \\`-._,-`-,\n                                      `._,._,'\n\nnf-core/tools version 2.0\n\nINFO     Linting pipeline: .                                                    lint.py:104\nINFO     Linting module: fastqc                                                 lint.py:106\n\n╭─────────────────────────────────────────────────────────────────────────────────╮\n│ [!] 1 Test Warning                                                              │\n╰─────────────────────────────────────────────────────────────────────────────────╯\n╭──────────────┬───────────────────────────────┬──────────────────────────────────╮\n│ Module name  │ Test message                  │ File path                        │\n├──────────────┼───────────────────────────────┼──────────────────────────────────┤\n│ fastqc       │ Local copy of module outdated │ modules/nf-core/modules/fastqc/  │\n╰──────────────┴────────────────────────────── ┴──────────────────────────────────╯\n╭──────────────────────╮\n│ LINT RESULTS SUMMARY │\n├──────────────────────┤\n│ [✔]  15 Tests Passed │\n│ [!]   1 Test Warning │\n│ [✗]   0 Test Failed  │\n╰──────────────────────╯\n```\n\n## Adding new modules\n\nIf you wish to contribute a new module, please see the documentation on the [nf-core website](https://nf-co.re/developers/modules#writing-a-new-module-reference).\n\n\u003e Please be kind to our code reviewers and submit one pull request per module :)\n\n## Help\n\nFor further information or help, don't hesitate to get in touch on [Slack `#modules` channel](https://nfcore.slack.com/channels/modules) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citation\n\nIf you use the module files in this repository for your analysis please you can cite the `nf-core` publication as follows:\n\n\u003e **The nf-core framework for community-curated bioinformatics pipelines.**\n\u003e\n\u003e Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso \u0026 Sven Nahnsen.\n\u003e\n\u003e _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n\n\u003c!---\n\n### Offline usage\n\nIf you want to use an existing module file available in `nf-core/modules`, and you're running on a system that has no internet connection, you'll need to download the repository (e.g. `git clone https://github.com/nf-core/modules.git`) and place it in a location that is visible to the file system on which you are running the pipeline. Then run the pipeline by creating a custom config file called e.g. `custom_module.conf` containing the following information:\n\n```bash\ninclude /path/to/downloaded/modules/directory/\n```\n\nThen you can run the pipeline by directly passing the additional config file with the `-c` parameter:\n\n```bash\nnextflow run /path/to/pipeline/ -c /path/to/custom_module.conf\n```\n\n\u003e Note that the nf-core/tools helper package has a `download` command to download all required pipeline\n\u003e files + singularity containers + institutional configs + modules in one go for you, to make this process easier.\n\n# New test data created for the module- sequenzautils/bam2seqz\nThe new test data is an output from another module- sequenzautils/bcwiggle- (which uses sarscov2 genome fasta file as an input).\n--\u003e\n\n# CI Runners\n\nWe are using self-hosted runners for the CI tests, managed via [RunsOn](https://runs-on.com/).\n","funding_links":[],"categories":["Nextflow"],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnf-core%2Fmodules","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fnf-core%2Fmodules","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnf-core%2Fmodules/lists"}