Overview

Overview

Develop nf-core pipelines

Components

Automated methods

Customize MultiQC methods descriptions
Creating components

Write modules and subworkflows
Cross organisational components

Use multi-organization modules
ext arguments

Configure tool-specific options
Meta maps

Store sample metadata
Setting custom remotes

Configure custom remotes

Containers

ARM64 on Bioconda

Enable ARM64 support for Bioconda packages
Seqera Containers

Use Seqera Containers

Documentation

Code formatting

Maintain consistent code style
Harshil alignment

Format Nextflow code for nf-core
Markdown

Use special content elements
Style guide

Follow nf-core style rules
Topic types

Understand documentation topic types

Institutional profiles

Overview

Write institutional profiles
Configuration

Structure institutional profile configuration
Documentation

Document institutional profiles
File structure

Create institutional profile files
nf-core/configs outside nf-core

Integrate profiles into custom workflows
Preparing to write

Prepare to write institutional profiles
Testing

Test institutional profiles

Migration guides

Migrating to topic channels

Migrate to topic channels

Pipelines

Adding modules

Add modules to pipelines
External use

Use nf-core code externally
Renaming branches

Switch default branch to main
Template files

Understand template elements

Template syncs

Overview

Keep pipelines up to date
Fixing a broken TEMPLATE branch

Fix a broken TEMPLATE branch
Manually syncing your pipeline

Sync pipeline with template manually
Merging automated PRs

Merge automated tool PRs
Setting up a pipeline sync retrospectively

Set up TEMPLATE branch

Testing

Overview

Test components with nf-test
Advanced

Write complex assertions
Assertions

Write test assertions