nf-core Tools CLI Reference

nf-core is a Python CLI for creating, linting, testing, and running nf-core-style pipelines, modules, and subworkflows. Target: 4.1.0, Python >=3.10,<4. Command signatures were checked against the installed release. Source: https://nf-co.re/docs/nf-core-tools and https://github.com/nf-core/tools/tree/4.1.0 . Remote downloads, scaffolding, schema web GUI and container runs below are illustrative; review before invoking.

Install

uv tool install "nf-core==4.1.0"
conda install -c bioconda nf-core
nf-core --version

In tools 4.1.0 the commands are grouped under pipelines, modules, subworkflows, and test-datasets. (Old flat commands such as nf-core lint have been removed and return an error.) Run nf-core --help or nf-core <group> --help to see current options, or nf-core interface for a graphical TUI command explorer.

For modules/subworkflows, group-level options go before the subcommand, e.g. to target a non-default component repo: nf-core modules -g <git-url> -b <branch> install fastqc.

Pipelines

Create a pipeline

nf-core pipelines create                # interactive: name, description, author
# non-interactive:
nf-core pipelines create --name mypipe --description "My pipeline" --author me

This generates the full nf-core template (see references/developing.md for the layout) with CI, linting, schema, and a test profile wired up. Develop on a feature branch; keep the TEMPLATE branch for sync.

Lint before pushing

cd my-pipeline
nf-core pipelines lint                   # run in the repo root
nf-core pipelines lint --release         # stricter checks for a release

Linting enforces nf-core structure, required files, schema/params consistency, module versions, and formatting. CI runs this on every PR.

Modules

Manage reusable process modules from the central nf-core/modules repo, or author your own.

# Reuse before you rebuild: install an existing module
nf-core modules install fastqc
nf-core modules install samtools/sort

# In a modules repository: author a new one, then lint + test it
nf-core modules create mytool
nf-core modules lint mytool
nf-core modules test mytool

In a pipeline repository, run nf-test test <test-path> directly for local/modified components. nf-core modules test is scoped to nf-core/modules-like repositories and rejects pipeline repositories.

Tool naming uses tool or tool/subtool (e.g. samtools/sort). Installed modules are pinned by git SHA in modules.json.

Subworkflows

Same lifecycle as modules, for chains of modules. Source: https://nf-co.re/docs

nf-core subworkflows install bam_sort_stats_samtools
nf-core subworkflows create align_bwa
nf-core subworkflows test align_bwa

Test datasets

nf-core test-datasets list-branches     # list test-data branches
nf-core test-datasets list              # list files on a selected branch
nf-core test-datasets search <term>     # find small test files in nf-core/test-datasets

Use these tiny, version-controlled files in module/pipeline tests (see references/testing.md).

Typical developer loop

nf-core pipelines create                       # scaffold
nf-core modules install fastqc                 # reuse community modules
nf-core modules create mytool                  # add a custom one
nf-test test path/to/main.nf.test               # test a local component in a pipeline
nf-core subworkflows install bam_sort_stats_samtools
nf-core pipelines schema build                 # keep schema in sync with params
nf-core pipelines lint                          # validate everything
prettier --write .                             # format (Harshil alignment)

See references/developing.md for what each generated file should contain, and references/testing.md for nf-test details.