nf-core Tools CLI Reference

nf-core is a Python CLI for creating, linting, testing, and running nf-core-style pipelines, modules, and subworkflows. Source: https://nf-co.re/docs/nf-core-tools

Install

bash

pip install nf-core            # PyPI
conda install -c bioconda nf-core
nf-core --version

In tools v3+ the commands are grouped under pipelines, modules, subworkflows, and test-datasets. (Older flat commands like nf-core create/nf-core lint still work but emit deprecation warnings — use the grouped form.) 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

Command	Purpose
`nf-core pipelines list [keywords]`	List/search nf-core pipelines (`--json`, `--sort`)
`nf-core pipelines create`	Scaffold a new pipeline from the template (interactive TUI; `--name --description --author` for non-interactive)
`nf-core pipelines launch <name>`	Interactive, schema-validated run command + params file
`nf-core pipelines download <name>`	Download pipeline + containers for offline use (`--revision`, `--container-system singularity`, `--outdir`)
`nf-core pipelines lint`	Lint the pipeline in the current dir against nf-core standards (`--release`, `--fix`, `--dir`)
`nf-core pipelines schema build`	Create/update `nextflow_schema.json` (opens a web editor)
`nf-core pipelines schema validate <pipeline> <params.json>`	Validate params against the schema
`nf-core pipelines schema lint`	Lint the schema file
`nf-core pipelines schema docs`	Generate parameter docs from the schema
`nf-core pipelines create-params-file <name>`	Generate a documented YAML params file
`nf-core pipelines bump-version <ver>`	Bump the pipeline version across files
`nf-core pipelines sync`	Merge template updates into a pipeline (TEMPLATE branch)
`nf-core pipelines rocrate`	Generate an RO-Crate metadata record
`nf-core pipelines create-logo <text>`	Render an nf-core-style logo

Create a pipeline

bash

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

bash

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.

Command	Purpose
`nf-core modules list remote [keyword]`	List modules available in nf-core/modules
`nf-core modules list local`	List modules installed in the current pipeline
`nf-core modules info <tool>`	Show a module's inputs/outputs/description
`nf-core modules install <tool>`	Install a module into `modules/nf-core/`
`nf-core modules update <tool>`	Update an installed module (`--all`, `--diff`)
`nf-core modules remove <tool>`	Remove an installed module
`nf-core modules patch <tool>`	Record local changes to an installed module as a patch
`nf-core modules create [tool]`	Scaffold a new module (`main.nf`, `meta.yml`, `tests/`)
`nf-core modules lint <tool>`	Lint a module against module specs
`nf-core modules test <tool>`	Run the module's nf-test suite
`nf-core modules bump-versions`	Bump tool versions in modules

bash

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

# Author a new one, then lint + test it
nf-core modules create mytool
nf-core modules lint mytool
nf-core modules test mytool

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

Command	Purpose
`nf-core subworkflows list remote/local`	List available/installed subworkflows
`nf-core subworkflows info <name>`	Show a subworkflow's interface
`nf-core subworkflows install <name>`	Install into `subworkflows/nf-core/`
`nf-core subworkflows update <name>`	Update an installed subworkflow
`nf-core subworkflows remove <name>`	Remove a subworkflow
`nf-core subworkflows create [name]`	Scaffold a new subworkflow
`nf-core subworkflows lint <name>`	Lint against subworkflow specs
`nf-core subworkflows test <name>`	Run the subworkflow's nf-test suite

bash

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

Test datasets

bash

nf-core test-datasets list              # list test-data branches
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

bash

nf-core pipelines create                       # scaffold
nf-core modules install fastqc                 # reuse community modules
nf-core modules create mytool                  # add a custom one
nf-core modules test mytool                    # nf-test it
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.