Overview

Overview

Developing nf-core pipelines

Components

Automated methods

Customize automated methods descriptions in MultiQC reports
Create components

Writing modules and subworkflows for nf-core
Cross organisational components

Use modules from multiple organisations in subworkflows
ext arguments

Configure tool-specific options in nf-core components
Meta maps

Storing sample metadata in nf-core components
Setting custom remotes

Set a custom remote for modules and subworkflows

Containers

ARM64 on Bioconda

Enabling existing Bioconda and Conda-forge packages to work on ARM64 architecture
Seqera Containers

Using Seqera Containers in nf-core modules

Documentation

Code formatting

Using Prettier and Ruff to maintain consistent code style
Harshil alignment

Formatting your Nextflow code to make nf-core core members happy
Markdown

Special content elements on nf-co.re
Style guide

nf-core style guide rules
Topic types

Documentation topic types

Institutional profiles

Overview

Write and contribute institutional configuration profiles
Configuration

Structuring your institutional profile configuration
Documentation

What to include in your institutional profile documentation
File structure

Which files to create or modify for your institutional profile
nf-core/configs outside nf-core

Integrating institutional profiles into custom workflows
Preparing to write

Information you need before creating an institutional profile
Testing

Testing your institutional profile before submission

Migration guides

Migrating to topic channels

Migrating nf-core modules and pipelines to use topic channels

Pipelines

Release procedure

A step-by-step guide for releasing a nf-core pipeline
Adding modules

Add nf-core modules to pipelines
External use

Guidelines for using nf-core code and infrastructure outside the organisation
Renaming branches

Switch your pipeline's default branch from master to main
Template files

Description of the elements of an nf-core template

Template syncs

Overview

How nf-core pipelines are kept up to date with community standards
Fixing a broken TEMPLATE branch

Fix a broken TEMPLATE branch
Manually syncing your pipeline

Manually synchronise your pipeline with the latest template
Merging automated PRs

Merge automated PRs after a new tools release
Setting up a pipeline sync retrospectively

Set up a correct TEMPLATE branch in your pipeline repository

Testing

Overview

Testing nf-core components with nf-test
Advanced

Complex assertion patterns and troubleshooting
Assertions

nf-core guidelines and common patterns