API

API

nf-core/tools API reference

CLI

Installation

Installation
TUI

Explore the nf-core command line graphically

Pipelines

create

Scaffolding a new pipeline using the nf-core template
list

Listing nf-core pipelines, local and remote
launch

Launch any Nextflow pipeline via TUI or GUI
create params file

Create a skeleton / template parameter file for a pipeline
download

Download a pipeline and its software dependencies.
licences

Automatically print software licences for DSL1 pipelines.
rocrate

Create a Research Object (RO) Crate
lint

Checking a pipeline against nf-core guidelines
schema

Building Nextflow schema files using a GUI
bump version

Bump a pipeline version number
sync

Sync a pipeline with the template
create logo

Create an nf-core pipeline logo

Modules

list

Listing nf-core modules, local and remote
info

Show information about a module
install

Install modules in a pipeline
update

Update modules in a pipeline
remove

Remove modules from a pipeline
patch

Create a patch file for a module
create

Create a new module
lint

Check a module against nf-core guidelines
test

Create a test for a module
bump versions

Bump bioconda and container versions of modules

Subworkflows

list

List subworkflows, locally installed and remove
info

Show information about a subworkflow
install

Install subworkflows in a pipeline
update

Update subworkflows in a pipeline
remove

Remove a subworkflow from a pipeline
create

Create a new subworkflow
lint

Check a subworkflow against nf-core guidelines
test

Create a test for a subworkflow

Test datasets

list

List module/pipeline test files from the nf-core/test-datasets
list branches

List branches on the nf-core/test-datasets repository for modules/pipeline test data
search

Search through module/pipeline test files in the nf-core/test-datasets repository on github