dev to main for 3.5.2 by mashehu · Pull Request #4015 · nf-core/tools

mashehu · 2026-01-30T13:56:01Z

No description provided.

…ific conventions

Fix wrong structure on version module failure tuple

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>

…x-meta-topic-fix

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>

Co-authored-by: nf-core-bot <[email protected]>

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: nf-core-bot <[email protected]>

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: nf-core-bot <[email protected]> Co-authored-by: Matthias Hörtenhuber <[email protected]>

…9f1c (#4009) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: nf-core-bot <[email protected]>

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: nf-core-bot <[email protected]> Co-authored-by: Matthias Hörtenhuber <[email protected]>

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: nf-core-bot <[email protected]>

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: nf-core-bot <[email protected]> Co-authored-by: Matthias Hörtenhuber <[email protected]>

Co-authored-by: Júlia Mir Pedrol <[email protected]> Co-authored-by: nf-core-bot <[email protected]>

* Update python:3.14-slim Docker digest to 9b81fe9 * [automated] Update CHANGELOG.md --------- Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: nf-core-bot <[email protected]>

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: nf-core-bot <[email protected]> Co-authored-by: Matthias Hörtenhuber <[email protected]>

Co-authored-by: Claude <[email protected]> Co-authored-by: nf-core-bot <[email protected]> Co-authored-by: mashehu <[email protected]>

Co-authored-by: nf-core-bot <[email protected]>

Co-authored-by: nf-core-bot <[email protected]> Co-authored-by: Matthias Hörtenhuber <[email protected]>

codecov · 2026-01-30T13:56:13Z

Codecov Report

❌ Patch coverage is 74.13793% with 45 lines in your changes missing coverage. Please review.
✅ Project coverage is 78.52%. Comparing base (d823888) to head (8a27fac).
⚠️ Report is 241 commits behind head on main.

Files with missing lines	Patch %	Lines
nf_core/pipelines/lint_utils.py	37.50%	25 Missing ⚠️
nf_core/components/lint/__init__.py	60.00%	4 Missing ⚠️
nf_core/modules/modules_json.py	0.00%	4 Missing ⚠️
nf_core/__main__.py	62.50%	3 Missing ⚠️
nf_core/components/nfcore_component.py	94.54%	3 Missing ⚠️
nf_core/modules/lint/meta_yml.py	88.46%	3 Missing ⚠️
nf_core/modules/modules_utils.py	40.00%	3 Missing ⚠️

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mashehu · 2026-01-30T13:57:30Z

@nf-core-bot update snapshots

mashehu · 2026-01-30T14:41:24Z

@nf-core-bot update snapshots

mashehu · 2026-01-30T14:55:13Z

@nf-core-bot update textual snapshots

mashehu and others added 30 commits November 13, 2025 20:55

switch pre-commit to prek for development

39d9b45

[automated] Update CHANGELOG.md

90c4d47

disable workspace setting for prek

3228738

use old CI id

5b7d1a6

Merge branch 'dev' into switch-to-trek

488e9d9

switch to experimental-cli for prettier

580711b

fix pre-commit hook installation in devcontainer

d32d9a0

Move contributing to docs/ and overhaul/review and add pipline-spec…

f7b967e

…ific conventions

Update CHANGELOG

1760476

Update CHANGELOG.md

a320047

switch changelog bot to prek

00ec0dd

add schema to devcontainer.json

fc04ade

[automated] Update CHANGELOG.md

4c1b8da

bump to 3.6.0dev

1d06ec6

[automated] Update CHANGELOG.md

3c48ea5

let lint --fix handle a missing topic entry in the meta.yml

9bde8f8

Fix wrong structure on version module failure tuple

b18aece

Add changelog entry

4f7945f

Apply suggestion from @mashehu

d2bb408

Apply suggestion from @mashehu

5b4d36f

Merge pull request #3920 from mashehu/bump-to-3.6.0dev

e04762e

Merge pull request #3923 from dialvarezs/fix-version-failure-tuple

586ed96

Fix wrong structure on version module failure tuple

Update actions/checkout action to v6 (#3921)

87a5039

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>

Merge branch 'dev' into fix-meta-topic-fix

cb5ff38

handle versions output channels

f89c575

add tests for multiple version channels

752b27e

add test for fixing missing topics

0e2ccda

Merge branch 'dev' of github.com:nf-core/tools into fix-meta-topic-fix

8b379c8

Merge branch 'fix-meta-topic-fix' of github.com:mashehu/tools into fi…

79d4aed

…x-meta-topic-fix

add disk clean-up step

2347489

renovate Bot and others added 22 commits January 28, 2026 13:25

Update GitHub Actions (#3971)

7470f7e

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>

Update docker/login-action digest to c94ce9f

82ad070

[automated] Update CHANGELOG.md

2ef9d0f

Simplify coverage reporting in pytest.yml (#3934)

137963f

Co-authored-by: nf-core-bot <[email protected]>

Update codecov/codecov-action digest to 671740a (#4000)

684a3a1

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: nf-core-bot <[email protected]>

Update dependency textual to v7 (#4008)

25cbc7c

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: nf-core-bot <[email protected]>

Update mcr.microsoft.com/devcontainers/base Docker tag to v2.1.5 (#4002)

194e74f

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: nf-core-bot <[email protected]> Co-authored-by: Matthias Hörtenhuber <[email protected]>

Update mcr.microsoft.com/devcontainers/miniconda Docker digest to 8a2…

3de78ad

…9f1c (#4009) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: nf-core-bot <[email protected]>

Update dependency textual-dev to v1.8.0 (#4005)

b526121

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: nf-core-bot <[email protected]> Co-authored-by: Matthias Hörtenhuber <[email protected]>

Update pre-commit hook astral-sh/uv-pre-commit to v0.9.28 (#4006)

b514c75

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: nf-core-bot <[email protected]>

Update pre-commit hook pre-commit/mirrors-mypy to v1.19.1 (#4007)

a55bf8d

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: nf-core-bot <[email protected]>

Update pre-commit hook astral-sh/ruff-pre-commit to v0.14.7 (#3943)

d256688

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: nf-core-bot <[email protected]> Co-authored-by: Matthias Hörtenhuber <[email protected]>

Update python:3.14-slim Docker digest to 119fd5b (#3910)

51230d5

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: nf-core-bot <[email protected]> Co-authored-by: Matthias Hörtenhuber <[email protected]>

handle type for val in topics correctly (#3991)

abcbd7c

Co-authored-by: Júlia Mir Pedrol <[email protected]> Co-authored-by: nf-core-bot <[email protected]>

Update python:3.14-slim Docker digest to 9b81fe9 (#4012)

ea17a00

* Update python:3.14-slim Docker digest to 9b81fe9 * [automated] Update CHANGELOG.md --------- Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: nf-core-bot <[email protected]>

Update pre-commit hook astral-sh/ruff-pre-commit to v0.14.14 (#4011)

b2be9ed

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: nf-core-bot <[email protected]> Co-authored-by: Matthias Hörtenhuber <[email protected]>

Add plain-text output option to lint commands (#3993)

350115e

Co-authored-by: Claude <[email protected]> Co-authored-by: nf-core-bot <[email protected]> Co-authored-by: mashehu <[email protected]>

fix failing devcontainer builds (#4013)

fef1c72

Co-authored-by: nf-core-bot <[email protected]>

fix wrong parsing when output values contain spaces (#3999)

255386b

Co-authored-by: nf-core-bot <[email protected]> Co-authored-by: Matthias Hörtenhuber <[email protected]>

Subworkflow lint bugfixes (#3968)

eeeb73f

Co-authored-by: nf-core-bot <[email protected]> Co-authored-by: Matthias Hörtenhuber <[email protected]>

bump to 3.5.2

12ce88e

remove template updates from patch

dcc91aa

mashehu requested a review from JulianFlesch January 30, 2026 13:56

JulianFlesch approved these changes Jan 30, 2026

View reviewed changes

update snapshots

8a27fac

mashehu merged commit fee44da into main Jan 30, 2026
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dev to main for 3.5.2#4015

dev to main for 3.5.2#4015
mashehu merged 203 commits intomainfrom
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