Add or update a module to nf-core/modules

• either to nf-core/modules for the nf-core community

• or to custom remotes as bigbio/nf-modules for internal use in bigbio/quantms (docs for custom remotes with nf-core tools here)

Getting started

• training of hello_nf-core

• tutorial in nf-core docs

• module specifications

Lint and test

Here for example for a local module called onsite in bigbio/nf-modules repo:

# Run linting checks on the local directory (-d .) for the "onsite" module
# This validates structure, metadata, schema, and best practices compliance (nf-core gudelines)
nf-core modules lint -d . onsite

# More linting automatically fixing issues where possible (--fix)
# Useful for quick formatting corrections and minor standard violations
nf-core modules lint --fix -d . onsite

# Run nf-test unit tests for the onsite module using Docker profile
# Ensures the module behaves as expected in a containerized environment
nf-test test --profile docker modules/bigbio/onsite/tests/main.nf.test

# Run tests and update the expected output snapshots
# Use this when intended changes would modify outputs (e.g., after code refactoring)
nf-test test --profile docker modules/bigbio/onsite/tests/main.nf.test --update-snapshot

# A note on --update-snapshot, do not use it if you have not verified the outputs

# nf-test is also available via nf-core tools cli:
nf-core modules test -d . --profile docker --update onsite

• more on snapshots: link