CLI Reference

code-to-module

Convert scripts and Git repos into submission-ready nf-core modules.

Usage:

code-to-module [OPTIONS] COMMAND [ARGS]...

Options:

  --help  Show this message and exit.

Subcommands

assess-only: Detect functionalities and assess complexity tier without generating modules.
bioconda-recipe: Generate a Bioconda recipe scaffold for a tool not yet in Bioconda.
containers: Discover and display all available container options for SOURCE.
convert: Convert SOURCE (file path or Git URL) into nf-core module(s).
update-standards: Update bundled nf-core standards to the latest version.

code-to-module assess-only

Detect functionalities and assess complexity tier without generating modules.

Usage:

code-to-module assess-only [OPTIONS] SOURCE

Options:

  --json                   Print JSON array to stdout.
  --docs TEXT              URL or local file path to documentation.
                           Repeatable.
  --existing-modules PATH  Path to an existing nf-core module directory.
                           Repeatable.
  --help                   Show this message and exit.

code-to-module bioconda-recipe

Generate a Bioconda recipe scaffold for a tool not yet in Bioconda.

Usage:

code-to-module bioconda-recipe [OPTIONS] SOURCE

Options:

  --tool-name TEXT  Override detected tool name.
  --outdir PATH     Directory to write meta.yaml.  [default: .]
  --help            Show this message and exit.

code-to-module containers

Discover and display all available container options for SOURCE.

Usage:

code-to-module containers [OPTIONS] SOURCE

Options:

  --functionality TEXT     Filter to one functionality by name.
  --json                   Print JSON array to stdout.
  --docs TEXT              URL or local file path to documentation.
                           Repeatable.
  --existing-modules PATH  Path to an existing nf-core module directory.
                           Repeatable.
  --help                   Show this message and exit.

code-to-module convert

Convert SOURCE (file path or Git URL) into nf-core module(s).

Usage:

code-to-module convert [OPTIONS] SOURCE

Options:

  --outdir TEXT                   Output directory for generated modules.
                                  [default: ./modules]
  --tier INTEGER                  Override complexity tier (1–5).
  --container [dockerfile|biocontainers|generate|stub]
                                  Override container selection.
  --no-interaction                Use default container silently (no menu
                                  shown).
  --dry-run                       Show what would be generated without writing
                                  files.
  --no-lint                       Skip post-generate lint checks.
  --no-update-check               Skip standards staleness check.
  --functionalities TEXT          Comma-separated functionality names to
                                  generate.
  --all-functionalities           Select all detected functionalities without
                                  prompting.
  --docs TEXT                     URL or local file path to documentation.
                                  Repeatable.
  --existing-modules PATH         Path to an existing nf-core module
                                  directory. Repeatable.
  --help                          Show this message and exit.

code-to-module update-standards

Update bundled nf-core standards to the latest version.

Usage:

code-to-module update-standards [OPTIONS]

Options:

  --help  Show this message and exit.

validate-module

Validate, fix, and review nf-core modules.

Usage:

validate-module [OPTIONS] COMMAND [ARGS]...

Options:

  --help  Show this message and exit.

Subcommands

fix: Propose and apply fixes for lint and nf-test failures.
review: Static analysis of a module against nf-core style conventions.
test: Run nf-core lint and nf-test against the module at MODULE_PATH.

validate-module fix

Propose and apply fixes for lint and nf-test failures.

Usage:

validate-module fix [OPTIONS] MODULE_PATH

Options:

  --from-report PATH  Load existing TestReport JSON instead of re-running
                      validation.
  --class-a-only      Only propose rule-based (Class A) fixes.
  -y, --yes           Auto-approve all Class A fixes (never auto-approves
                      Class B).
  --no-revalidate     Skip re-validation after applying fixes.
  --help              Show this message and exit.

validate-module review

Static analysis of a module against nf-core style conventions.

Usage:

validate-module review [OPTIONS] MODULE_PATH

Options:

  --errors-only       Show only ERROR severity items.
  --json-output PATH  Write ReviewReport as JSON to PATH.
  --help              Show this message and exit.

validate-module test

Run nf-core lint and nf-test against the module at MODULE_PATH.

Usage:

validate-module test [OPTIONS] MODULE_PATH

Options:

  --lint-only         Run nf-core lint only.
  --nftest-only       Run nf-test only.
  --json-output PATH  Write TestReport as JSON to PATH.
  --help              Show this message and exit.