Overview

Overview

Guidelines and requirements for nf-core contributions and best practices.

Components

Overview

Write nf-core components

Modules

General

Follow general module guidelines

Naming conventions

Follow naming conventions

Input/output Options

Define module inputs and outputs

Documentation

Document modules

Parameters

Use module parameters

Resource requirements

Specify resource requirements

Software

Specify software dependencies

Testing

Test modules

Formatting

Nextflow code formatting requirements

Subworkflows

General

Follow general subworkflow specifications

Naming conventions

Follow naming conventions

Input output options

Define subworkflow inputs and outputs

Subworkflow parameters

Use subworkflow parameters

Documentation

Document subworkflows

Testing

Test subworkflows

Formatting

Nextflow code formatting requirements

Pipelines

Overview

Specifications for nf-core pipelines

Recommendations

Bioconda

Package software using bioconda and biocontainers.

Build with community

Package software using bioconda and biocontainers.

Cloud compatible

Pipelines should be tested on cloud computing environments.

Custom containers

What to do with custom containers that are hosted on docker.io or ghcr.io

DOIs

Pipelines should have digital object identifiers (DOIs).

File formats

Use community accepted modern file formats.

Publication credit

Recognition for nf-core pipeline publications

Testing

Use nf-test to validate pipeline

Requirements

Acknowledgements

Pipelines must properly acknowledge prior work.

CI testing

Pipelines must run CI tests.

Community owned

Pipelines are owned by the community.

Docker

Software must be bundled using Docker and versioned.

Documentation

Pipeline documentation must be hosted on the nf-core website

Git branches

Use `master|main`, `dev` and `TEMPLATE`.

Identity branding

Primary development must on the nf-core organisation.

Keywords

Excellent documentation and GitHub repository keywords.

Linting

The pipeline must not have any failures in the `nf-core pipelines lint` tests

Minimum inputs

Pipelines should be able to run with as little input as possible.

MIT license

Pipelines must open source, released with the MIT license.

Nextflow

Pipelines must be built with Nextflow

Parameters

Strive to have standardised usage.

RO Crate

Pipelines must come with their own Research Object (RO) Crate

Semantic versioning

Pipelines must use semantic versioning.

Single command

Pipelines should run in a single command.

Use the template

All nf-core pipelines must be built using the nf-core template.

Workflow name

Names should be lower case and without punctuation.

Workflow size

Not too big, not too small

Workflow specificity

There should only be a single pipeline per data / analysis type.

Reviews

Overview

Best practices for reviewing contributions
Request reviewers

Best practices for requesting and engaging reviewers
Rapid merge

Guidelines for merging pull requests after approval
Review scope

Guidelines for managing review feedback and resolution
Commit strategy

Best practices for managing commits and merges

Test data

Overview

Specifications for managing test data in nf-core
General

General guidelines for nf-core test data
Modules

Test data guidelines specific to nf-core modules