Releases: nf-core/tools
v3.3.2 - Tungsten Tamarin Patch 2
v3.3.2 - Tungsten Tamarin Patch 2 - [2025-07-08]
Template
- Avoid overriding
NFT_DIFF
andNFT_DIFF_ARGS
innf-test
action (#3606) and (#3619) - fix nf-test scope to ignore nf-core module/swf tests (#3609)
- write github.run_id on pipeline template (#3637)
- Bump nf-schema to
2.4.2
(#3533) - Bump the minimal Nextflow version to
24.10.5
(#3533, #3667) - CI - Only trigger nf-test action on pull_request (#3628)
- Fix link to nf-test GHA in README.md (#3630)
- Add accelerator directive for GPU-enabled processes (#3632)
- Update dependency prettier to v3.6.0 (#3641) and 3.6.2 (#3646)
- Add opt-in feature
gpu
(#3562) - Update zentered/bluesky-post-action action to v0.3.0 (#3626)
Linting
- Fix linting of nf-test files content (#3603)
Modules
- Remove args stub from module template to satisfy language server (#3403)
- Fix modules meta.yml file structure (#3532)
- Fix wrong key when updating module outputs (#3665)
Subworkflows
General
- update id of ruff hook in pre-commit config (#3621)
- Fixes a bug with the test-datasets subcommand #3617
- Pin python Docker tag to f2fdaec (#3623)
- Make changelog bot push to correct remote (#3638)
- Give unique button ids to help buttons in create app (#3645)
- Parallelize pytest runs and speed up coverage step (#3635)
- Update gitpod/workspace-base Docker digest to 77021d8 (#3649)
- Update error message for rocrate_readme_sync (#3652)
- Update
nf-core modules info
command aftermeta.yml
restructuring (#3659) - Enable parsing of multi-line config values (#3629)
Version updates
v3.3.1 - Tungsten Tamarin Patch
v3.3.1 - Tungsten Tamarin Patch - [2025-06-02]
This patch release includes fixing a comment message in the nf-test.yml GitHub Action.
Template
- Use correct comment symbol in
nf-test.yml
(#3601)
v3.3.0 - Tungsten Tamarin
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.
Template
- Remove the on
pull_request_target
trigger andpull_request
types from the download test. Also droppush
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)
Linting
- 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
andRO-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)
Subworkflows
- Install subworkflows with modules from different remotes (#3083)
Modules
- Increase meta index for multiple input channels (#3463)
- Configure the default module repository, branch, and path from environment variables. (#3481)
General
- 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)
Version updates
- 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)
v3.2.1 - Pewter Pangolin Patch
v3.2.1 - Pewter Pangolin Patch - [2025-04-30]
This patch release fixes pipelines CI, particularly the GitHub Action to launch full-size tests on AWS.
There was also an error when running the pipelines with the edge version of Nextflow. Due to this, we had to downgrade the version of the nf-schema plugin until the compatibility with the latest Nextflow is addressed. Now, running the pipeline with Nextflow latest-everything
won't fail, to avoid future similar problems, until we find a better way to test edge versions.
Template
v3.2.0 - Pewter Pangolin
v3.2.0 - Pewter Pangolin - [2025-01-27]
Highlights
- Local modules and subworkflows now use a template with a
tests/
directory, similar to the components created for the nf-core/modules. - We fixed the permission error bug when running nf-core pipelines with the Nextflow version
24.12.0-edge
. - We removed the automated pipeline release tweets. There are still automated Mastodon and Bluesky posts.
Template
- Remove automated release tweets (#3419)
- Update template components (#3426)
- Fix
process.shell
innextflow.config
(#3416) and split into new lines (#3425)
Modules
- Modules created in pipelines "local" dir now use the full template (#3256)
Subworkflows
- Subworkflows created in pipelines "local" dir now use the full template (#3256)
General
v3.1.2 - Brass Boxfish Patch
v3.1.2 - Brass Boxfish Patch - [2025-01-20]
Template
Download
- Allow
nf-core pipelines download -r
to download commits (#3374) - Fix faulty Download Test Action to ensure that setup and test run as one job and on the same runner (#3389)
Modules
- Fix bump-versions: only append module name if it is a dir and contains
main.nf
(#3384)
General
v3.1.1 - Brass Boxfish Patch
This patch release includes fixing the nf-core pipelines bump-version
command and adding back to the pipeline template including the modules.config
file.
Template
- Use outputs instead of the environment to pass around values between steps in the Download Test Action (#3351)
- Fix pre commit template (#3358)
- Set LICENSE copyright to nf-core community (#3366)
- fix including modules.config (#3356)
Linting
- Linting of pipeline LICENSE file is a warning to allow for author/maintainer names (#3366)
General
v3.1.0 - Brass Boxfish
⭐ Highlights ⭐
- We added the new
contributors
field to the pipeline templatemanifest
. - The
nf-core pipelines download
command supports ORAS container URIs. - New command
nf-core subworkflows patch
.
Template
- Keep pipeline name in version.yml file (#3223)
- Fix Manifest DOI text (#3224)
- Do not assume pipeline name is url (#3225)
- fix
workflow_dispatch
trigger and parse more review comments in awsfulltest (#3235) - Add resource limits to Gitpod profile(#3255)
- Fix a typo (#3268)
- Remove
def
fromnextflow.config
and addtrace_report_suffix
param (#3296) - Move
includeConfig 'conf/modules.config'
next toincludeConfig 'conf/base.config'
to not overwrite tests profiles configurations (#3301) - Use
params.monochrome_logs
in the template and update nf-core components (#3310) - Fix some typos and improve writing in
usage.md
andCONTRIBUTING.md
(#3302) - Add
manifest.contributors
tonextflow.config
(#3311) - Update template components (#3328)
- Template: Remove mention of GRCh37 if igenomes is skipped (#3330)
- Be more verbose in approval check action (#3338)
Download
- First steps towards fixing #3179: Modify
prioritize_direct_download()
to retain Seqera Singularityhttps://
Container URIs and hardcode Seqera Containers intogather_registries()
(#3244). - Further steps towards fixing #3179: Enable limited support for
oras://
container paths (only absolute URIs, no flexible registries like with Docker) and prevent unnecessary image downloads for Seqera Container modules withreconcile_seqera_container_uris()
(#3293). - Update dawidd6/action-download-artifact action to v7 (#3306)
Linting
- allow mixed
str
anddict
entries in lint config (#3228) - fix
meta_yml
linting test failing due tomodule.process_name
always being""
(#3317) - fix module section regex matching wrong things (#3321)
Modules
- add a panel around diff previews when updating (#3246)
Subworkflows
- Add
nf-core subworkflows patch
command (#2861) - Improve subworkflow nf-test migration warning (#3298)
General
- Include
.nf-core.yml
innf-core pipelines bump-version
(#3220) - create: add shortcut to toggle all switches (#3226)
- Remove unrelated values when saving
.nf-core
file (#3227) - use correct
--profile
options fornf-core subworkflows test
(#3233) - Update GitHub Actions (#3237)
- add
--dir/-d
option to schema commands (#3247) - fix headers in api docs (#3323)
- handle new schema structure in
nf-core pipelines create-params-file
(#3276) - Update Gitpod image to use Miniforge instead of Miniconda(#3274)
- Add hint to solve git errors with a synced repo (#3279)
- Run pre-commit when testing linting the template pipeline (#3280)
- Make CLI prompt less nf-core specific (#3326)
- Update gitpod vscode extensions to use nf-core extension pack (#3327)
- Remove toList() channel operation from inside onComplete block (#3304)
- build: Setup VS Code tests (#3292)
- Don't break gitpod.yml with template string (#3332)
- rocrate: remove duplicated entries for name and version (#3333)
- rocrate: Update crate with version bump and handle new contributor field (#3334)
- set default_branch to master for now (#3335)
- Set git defaultBranch to master in sync action (#3337)
- Add verbose mode to sync action (#3339)
Version updates
v3.0.2 - Titanium Tapir Patch
This patch release fixes some bugs found in the pipeline template.
Template
- Add null/ to .gitignore (#3191)
- Parallelize pipeline GHA tests over docker/conda/singularity (#3214)
- Fix
template_version_comment.yml
github action (#3212) - Fix pre-commit linting on pipeline template (#3218)
Linting
- Fix bug when linting schema params and when using
defaultIgnoreParams
(#3213)
General
v3.0.1 - Titanium Tapir Patch
Template
- Fixed an issue where the linting CI action didn't read the correct file (#3202)
- Fixed condition for
awsfulltest
to run (#3203) - Fix too many empty lines added by jinja (#3204 and #3206)
- Fix header blocks in local subworkflow including git merge marker-like strings (#3201)
- Update included subworkflows and modules (#3208)