Release v3.3.0 - Tungsten Tamarin · nf-core/tools

v3.3.0 - Tungsten Tamarin - [2025-06-02]

Highlights

This version adds pipeline level nf-test to the pipeline template.
We also enabled to install subworkflows with modules from different remotes.

Remove the on pull_request_target trigger and pull_request types from the download test. Also drop push triggers on other CI tests. (#3399)
Add nf-core template version badges to README (#3396)
Basic pipeline level nf-test tests (#3469, 3597)
Add Bluesky badge to readme (#3475)
Add .nftignore to trigger list (#3508)
Tun nf-test tests on runsOn runners (#3525)
Include the centralized nf-core configs also in offline mode, if a local copy is available. (#3491)
Make jobs automatically resubmit for exit code 175 (#3564)
Bump nf-schema back to 2.3.0 (#3577)
Do not skip AWS fulltest action on release (#3583)
Make all github actions in the template kebab-case (#3600)

Add linting for ifEmpty(null) (#3411)
Fix arbitrarily nested params schema linting (#3443)
Fix linting with comments after the input directive (#3458)
EDAM ontology fixes (#3460)
Fix default linting of nf-core components when nf-core pipelines lint is ran (#3480)
Fix the unexpected warning and sychronize the README.md and RO-crate-metadata.json (#3493)
Adapt the linter to the new notation used to include the centralized nf-core configs (#3491)
Addressing more cases than can happen when processing input and output values (#3541)
Add linting of nf-test files content (#3580)

Increase meta index for multiple input channels (#3463)
Configure the default module repository, branch, and path from environment variables. (#3481)

Remove hard coded key prefix for schema in launcher (#3432)
Output passed to write_params_file as Path object (#3435)
format name/value with YAML syntax (#3442)
Remove Twitter from README (#3454)
docs: fix contributing link in the main README (#3459)
Cleanup: Removed Redundant if Condition (#3468)
Ontology fix comment yaml (#3502)
Bugfix - add back logo to the README (#3504)
Update dead link (#3505)
Changing retrieval of file extension from EDAM (#3512)
Refactor adding EDAM ontologies and allowing detect more patterns (e.g., versions.yml) (#3519)
Add offline configs test action (#3524)
Adds test-datasets subcommand for listing/searching files in the nf-core/test-datasets repo from the cli (#3487, #3548, #3566, #3567)
Fix indentation in included_configs API docs (#3523)
Adding boundary in regex (#3535)
Switch to using runsOn runners in nf-core/tools repo (#3537)
Handling issue with arity #3530 (#3539)
GitHub action for nightly tests with Nextflow from source (#3553)
Update CI to test template pipelines with nf-test (#3559)
Use secret for notification email on nextflow nightly builds (#3576)
Use pdiff from setup-nf-test (#3578)

chore(deps): update python:3.12-slim docker digest to fd95fa2 (#3587)
chore(deps): update dependency pytest-textual-snapshot to v1.1.0 (#3439)
chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.11.11 (#3585)
chore(deps): update pre-commit hook editorconfig-checker/editorconfig-checker.python to v3.2.0 (#3446)
chore(deps): update pre-commit hook pre-commit/mirrors-mypy to v1.15.0 (#3447)
Update prettier to 3.5.0 (#3448)
chore(deps): update gitpod/workspace-base docker digest to 3aa18f4 (#3586)
chore(deps): update github actions (#3488)
chore(deps): update github actions (#3498)
chore(deps): update dependency textual to v2 (#3471)
chore(deps): update actions/setup-python digest to 8d9ed9a (#3518)
chore(deps): update actions/github-script action to v7 (#3545)
chore(deps): pin dependencies (#3554)
chore(deps): update codecov/codecov-action digest to 18283e0 (#3575)