Releases

General

Remove unnecessary default branch detection from sync action (#4540)
Make the changelog action react a bit more and harden its security (#4544)

Modules

Keep the full name of local TOOL/SUBTOOL components in nf-core modules lint and nf-core modules containers create (#4541)

Template

Pin our own controlled actions to major version to get faster updates (#4543)

Highlights:

Metro maps with manifest.diagram in the nextflow.config file
New command: nf-core pipelines containers create-configs

General

Fixes bug in test-datasets list related to broken rich import (#4477)
Add nf-core pipelines containers create-configs to regenerate the pipeline conf/containers_*.config files (#XXXX)
update update-*-snapshot actions to more robust way (#4509)

Linting

Warn if manifest.diagram is not set, and fail if it is not a relative path to an existing image file (#4460)
Add strandeness to permitted meta keys (#4473)
remove ext.use_gpu as a permitted ext key, superseded by task.accelerator (#4445)
fix(lint): use repo-root-relative path in git restore call in container_configs (#4301)
Fix subworkflow lint parsing sibling subworkflow include statements (#4527)

Modules

modules main.nf template: match nf-core container formatting in main.nf (#4459)

Template

remove redundant ext.use_gpu from the process_gpu label, use accelerator only (#4445)
Switch to using fix-linting.yml workflow from nf-core/actions repo, to avoid leakage of nf-core bot token and rename it from fix_linting.yml to fix-linting.yml (#4485)
Add a commented-out manifest.diagram to nextflow.config, for the pipeline metro map (#4460)
git-ignore nf-test files (#4461)
Bump nf-schema to 2.7.3 to allow running pipelines with Nextflow 26.04 (#4463)
Bump nft-utils to 1.2.1, matching nf-core/modules (#4489)
VSCode: add recommended extensions, fix link to admonition styling CSS for markdown previews (#4455)
Pin action-tower-launch to v2 (#4502)
Pin nf-schema version in awsfulltest (#4501)
Don't block workflow.onComplete on the MultiQC report (#4486)

General

container configs: use correct key for conda configs (#4269)
Coerce launch params_out to Path to fix AttributeError (#4299) (#4317)
generate valid Markdown when piping schema docs to file (#4319)
fix API docs bug in pydantic autodoc (#4320)
Improve CLI startup speed (#4383)

Linting

accept process_low_memory as a standard module label (#4264)
improve linting for modules.json to add support for only installing subworkflows from a repository and provide more explicit error messages (#4287)
improve singularity_tag linting check (add skip, handle exceptions correctly, check against oras) (#4358)
make regex for meta keys more specific to avoid false positives (#4280)

Modules

modules info: handle one element channels correctly (#4268)
module lint for module name matching against nf-core module naming specifications (#4325)
Clarify execution context of nf-core modules test command (#4346)
Add nf-core modules containers create to build module containers via Seqera Wave and record them in the containers: section of meta.yml (#3954)
Add a log hint in modules create for create containers and switch modules bump-versions to use Seqera containers (#4374)

Template

New pre-commit hooks blocking large files and merge markers in pipeline template (#3935)
add process_low_memory resource label to base.config (#4264)
Simpler test data path in tests/nextflow.config (#4285)
fix dead link (#4307)
remove date placeholder from changelog title (#4333)
correct always-true nf-core pipelines lint condition in the linting workflow and fix doc typos (broken #lint-tests anchor, duplicate word, stray code-span space) (#4324)
Fix publishDir configuration in modules.config for multiqc (#4347)
Switch to a more secure approach for PR comments by splitting the GitHub Actions workflow (#4342)

Download

Included support for Apptainer in nf-core pipelines download --container-system apptainer (#4352)

Version updates

Update pre-commit hook pre-commit/mirrors-mypy to v2 (#4270)
Update pre-commit npm dependencies to v3.8.4 (#4335)

v4.0.3 - Bold Boa Patch 3

This is a security patch to prohibit leakage of a GitHub Token through certain GitHub Action workflows.

Template

Switch to a more secure approach for PR comments by splitting the GitHub Actions workflow (#4342)
Add pr-comment for nf-test silent failures with latest-everything (#4414)

General

Fix pytest for strict nextflow syntax (#4261)
Fix CI: commit updated configs after modules update step (#4292)

v4.0.2 - Bold Boa Patch 2 - [2026-04-30]

General

add pipeline_dir to search directories for include statements (#4252)

Template

fix version capture in downloads_action (#4251)
Remove format constraint for igenomes_base (#4253)

v4.0.1 - Bold Boa Patch - [2026-04-29]

General

handle prek not being exposed to $PATH (#4238)
fix failing api doc generation script (#4239)
switch changelog bot trigger only on comments (#4241)
fix indentation in generated api docs (#4245)

Modules

allow task.ext.prefix2 in modules linting (#4234)

v4.0.0 - Bold Boa - [2026-04-28]

See more details about this release on our blog: https://nf-co.re/blog/2025/tools-4_0_0

Highlights

Nextflow strict syntax in the pipeline template
Auto-generated container config files
New command aliases
Webhook notifications removed

Breaking Changes

require strict Nextflow syntax
dropped deprecated prefix-free commands, e.g. nf-core create is now nf-core pipelines create
removed the --migrate-pytest functionality for nf-core modules create

General

Add command to generate pipeline container config files (#3955)
sync: don't overwrite the defaultBranch if already set in nextflow.config (#3939)
Add aliases to common sub-subcommands like install, lint, etc. (#3980)

Command	Subcommand	Aliases
`modules` & `subworkflows`	`bump-versions` (modules only)	`bump-version`, `bump`, `bv`, `b`
	`create`	`c`
	`install`	`add`, `i`
	`lint`	`l`
	`list`	`ls`
	`patch`	`p`
	`remove`	`uninstall`, `rm`
	`test`	`t`
	`update`	`up`, `u`
`pipelines`	`bump-version`	`bump`, `bv`, `b`
	`create`	`c`
	`download`	`d`
	`lint`	`l`
	`list`	`ls`
	`schema lint`	`schema l`
	`sync`	`s`
`test-datasets`	(command group)	`test-dataset`, `tds`, `td`, `t`
	`list`	`ls`
	`list-branches`	`lsb`

Add more ruff rules (B, PTH, RSE, SIM, C4, BLE, A) (#4034)
hinder renovate from updating packages with a fixed range (#4058)
nf-core bot: collect all snapshots before commiting (#4082)
fix nf-core bot snapshot action (#4083)
Fix GHA notification for AWS full tests job (#4092)
Parse manifest.contributors to fill in the RO-Crate (#4147)
Isolate test runs to avoid cross talks of Nextflow assets (#4175)
Remove --migrate-pytest functionality and deprecated pipeline commands (#4167)
use prek instead of pre-commit in all instances (#4187)
nextflow source CI: set up uv (#4208)
automatically handle merge conflicts for changelog files with union (#4223)

Download

Fix nf-core pipelines download --platform output directory structure and tagging (#4185)
Add a fallback for nextflow inspect for pipelines without a default for the --outdir parameter specified in the test profiles (#4212)

Linting

fix failing pytest for lint after samtools topic conversion (#4026)
capture correct error for invalid .nf-core.yml (#4080)
Ensure release linting happens on branch named main (#4121)
Add linting for meta and ext keys (#4127)
Add strict syntax linting to template with pre-commit (#4128)
Lint meta variable names (#4129)
Lint against the correct repo (#4140)
Fix false positive matches to words like text in ext key linting (#4142)
Fix changelog bot failing after linting step (#4155)
lint for correct syntax for compressed files in stubs (#4048)
fix linting with missing input (#4202)
fix(lint): use correct config key zenodo_doi (#4201)
add missing lint test documentation and add pre-commit check for them (#4052)

Modules

fix incorrect unqoting of val() version numbers (#4042)
Template: have a main: section in workflow even when modules are skipped (#4043)
allow harshil alignment™ in version channels (#4064)
Update example links in main.nf comments (#4188)
Always prettify modules.json (#4063)
Allow versions.yml in the version topics (#4094)
switch to gitlab module to test with old version syntax (#4126)
linting: Fix version emit for version.yml (#4095)
linting: make version topics mandatory (#4163)
only check for compressed stubs with .gz as final extension (#4206)
modules linting: require registry prefix in container link (#4209)
add apptainer support to module template (#4210)

Subworkflows

update test to new upstream subworkflow structure (#4038)< 8000 /li>
Fix lint: preserve underscores for subworkflow includes via full path (#4074)
update modules and subworkflows in template (#4077)
add --force parameter to modules remove and subworkflow remove (#4213)

Template

Remove webhook notifications (hook_url, slackreport, adaptivecard) (#4051).
- Use specific nextflow plugins instead:
  - nf-slack
  - nf-teams
Add .lineage/ directory to the template .gitignore (#4075).
Update nf-test module template to topics (#4113)
Fix nf-core tools version to what is specified in .nf-core.yml for the GitHub workflow download_pipeline.yml (#4124).
Update all documentation URLs to point to equivalents on the new nf-core website documentation structure (#4135)
Trigger full nf-test run if scripts in bin/ or schema JSON files are modified (#3897)
Add additional fusion specific exit codes (#4180)
fix: rename variables in pipeline nf-test template default.nf.test for clarity (#4189)
bump nextflow to 25.10.4 (#4190)
fix jinja variable in template (#4156)
fix some nextflow lint warnings in different skipped template versions (#4191)
trigger full nf-test run if CI changes (#4203)
Include AI and LLM usage guidelines in CONTRIBUTING.md (#4211)

Version updates

Update GitHub Actions (#4001)
Update dependency prettier to v3.8.1 (#4003)
Update dawidd6/action-download-artifact action to v14 (#4018)
Update mcr.microsoft.com/devcontain...

v3.5.2 - Terne Topi Patch 2 - [2026-01-30]

General

Switch from pre-commit to prek for pre-commit hooks in development(#3899)
Fix docker errors in test (#3924)
switch to uv and pyproject.toml (#3925)
dockerhub action: add disk clean-up step and combine the two actions (#3926)
Pin j178/prek-action action to 91fd7d7 (#3931)
Simplify coverage reporting in pytest.yml (#3934)
add pre-commit hook to keep uv.lock in sync (#3933)
Fix quote handling in meta.yml (#3948)
Add support for SVG files in bump-version command (#3978)
handle type for val in topics correctly (#3991)
Update docker/login-action digest to c94ce9f (#3998)
fix wrong parsing when output values contain spaces (#3999)
fix failing devcontainer builds (#4013)

Linting

fix test for linting for version.yml (#39 8000 47)
Fix bugs in subworkflows lint causing false positive warnings (#3968)
more fixes for incorrect parsing of version statement (#3973)
handle val in version topics correctly (#3988)
handle additional attributes in input parsing correctly (#3990)

Modules

sort meta.yml based on keys in schema (#3958)
fix(modules_json): Use name string instead of dict as key in recreate_dependencies (#3963)
linting: polish regex for output parsing in modules main.nf (#3967)
modules linting: catch failing edamontology requests (#3994)

Subworkflows

Update to new topic version handling (#3929)

Version updates

Update actions/setup-python digest to 83679a8 (#3928)
Update python:3.14-slim Docker digest to 119fd5b (#3910)
Update pre-commit hook astral-sh/ruff-pre-commit to v0.14.7 (#3943)
Update mcr.microsoft.com/devcontainers/miniconda Docker digest to 2be0f5a (#3946)
Update actions/checkout digest to 8e8c483 (#3956)
Update GitHub Actions (#3957)
Update astral-sh/setup-uv digest to ed21f2f (#3959)
Update codecov/codecov-action digest to 671740a (#3962)
Update codecov/codecov-action digest to 671740a (#4000)
Update pre-commit hook pre-commit/mirrors-mypy to v1.19.1 (#4007)
Update pre-commit hook astral-sh/uv-pre-commit to v0.9.28 (#4006)
Update dependency textual-dev to v1.8.0 (#4005)
Update mcr.microsoft.com/devcontainers/base Docker tag to v2.1.5 (#4002)
Update dependency textual to v7 (#4008)
Update mcr.microsoft.com/devcontainers/miniconda Docker digest to 8a29f1c (#4009)
Update pre-commit hook astral-sh/ruff-pre-commit to v0.14.14 (#4011)
Update python:3.14-slim Docker digest to 9b81fe9 (#4012)

v3.5.1 - Terne Topi Patch 1 - [2025-11-19]

General

Fix blog_post parameter for nf-core pipelines sync command (#3911)
Fix markdown in sync PR message (#3913)

v3.5.0 - Terne Topi - [2025-11-19]

See more details about this release on our blog: https://nf-co.re/blog/2025/tools-3_5_0

Highlights

Version reporting with topic channels in modules

General

Improve file ignores in workflow file enumeration (#3820)
add optional link to blogpost to sync PR (#3852)
Avoid deleting files ignored by git during pipelines sync (#3847)
remove trailing comas from nextflow_schema.json (#3874)
Make bump-version snapshot test more stable (#3865)
add missing setup steps to snapshot update action (#3883)
fix sync test (#3885)
fix syntax in dockerfile for devcontainer (#3887)
Enable authenticated pipeline download from nf-core compatible repos with github api (#3607)
fix pytest setup matrix (#3888)
Fix GH API rate limits. (#3895)
devcontainer: downgrade to debian 12 and revert #3904 (#3907)

Template

Change GitHub Codespaces badge style (#3869 and #3873)
update multiqc version to fix utils test (#3853)
Update multiqc to 1.32 (#3878)
Update pipeline creation information page to be more exclusive as to what should use the full nf-core pipeline template (#3891)
Fix LSP warnings in pipeline template (#3905)

Linting

TEMPLATE: ignore nf-core components during prettier linting (#3858)
update json schema store URL (#3877)
add word boundary for input, output and topic linting (#3894)
Add linting of topics (#3902)

Modules

Add topics to the template + update linting (#3779)
Preserve the value of self.modules_repo across nested calls (#3881)
modules lint: handle meta.ymls without topics field (#3909)

Version updates

Update GitHub Actions (major) (#3849)
Update docker/setup-qemu-action digest to c7c5346 (#3875)
chore(deps): update python:3.14-slim docker digest to 9813eec (#3880)
chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.14.4 (#3882)
Update python:3.14-slim Docker digest to 4ed3310 (#3862)
Update dependency textual-dev to v1.8.0 (#3860)
Update pre-commit hook astral-sh/ruff-pre-commit to v0.14.3 (#3861)
Update GitHub Actions (major) (#3849)
chore(deps): update mcr.microsoft.com/devcontainers/miniconda docker digest to 19516ba (#3890)
Update dependency textual to v6.6.0 (#3892)
chore(deps): update mcr.microsoft.com/devcontainers/base:debian docker digest to 2e826a6 (#3893)
Update pre-commit hook astral-sh/ruff-pre-commit to v0.14.5 (#3900)
Update actions/checkout digest to 93cb6ef (#3906)

v4.2.1 - Metropolitan Mouse Patch 1

General

Modules

Template

Uh oh!

v4.2.0 - Metropolitan Mouse

Highlights:

General

Linting

Modules

Template

Uh oh!

v4.1.0 - Marshalled Mamba

General

Linting

Modules

Template

Download

Version updates

Uh oh!

4.0.3 - Bold Boa Patch 3

v4.0.3 - Bold Boa Patch 3

Template

General

Uh oh!

4.0.2 - Bold Boa Patch 2

v4.0.2 - Bold Boa Patch 2 - [2026-04-30]

General

Template

Uh oh!

v4.0.1 - Bold Boa Patch

v4.0.1 - Bold Boa Patch - [2026-04-29]

General

Modules

Uh oh!

v4.0.0 - Bold Boa

v4.0.0 - Bold Boa - [2026-04-28]

Highlights

Breaking Changes

General

Download

Linting

Modules

Subworkflows

Template

Version updates

Uh oh!

v3.5.2 - Terne Topi Patch 2

v3.5.2 - Terne Topi Patch 2 - [2026-01-30]

General

Linting

Modules

Subworkflows

Version updates

Uh oh!

v3.5.1 - Terne Topi Patch 1

v3.5.1 - Terne Topi Patch 1 - [2025-11-19]

General

Uh oh!

v3.5.0 - Terne Topi

v3.5.0 - Terne Topi - [2025-11-19]

Highlights

General

Template

Linting

Modules

Version updates

Uh oh!