`dev` to `main` for 4.0.0 by mashehu · Pull Request #4225 · nf-core/tools

mashehu · 2026-04-27T13:33:24Z

No description provided.

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

Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

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

# Conflicts: # CHANGELOG.md

* improve debug logging * make sure to not unqote val entries, to avoid number-string confusion * add test * [automated] Update CHANGELOG.md * Update nf_core/modules/lint/meta_yml.py Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com> * removed unneeded try except * update uv deps * pin setuptools to <81 to support refgenie --------- Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>

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

* Update python:3.14-slim Docker digest to 486b809 * [automated] Update CHANGELOG.md * [automated] Fix code linting --------- Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

* Lock file maintenance * [automated] Update CHANGELOG.md --------- Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: nf-core-bot <core@nf-co.re>

* Update actions/stale digest to b5d41d4 * [automated] Update CHANGELOG.md --------- Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: nf-core-bot <core@nf-co.re>

Topic version warnings

Replace the old webhook-based Slack/Teams notification system (hook_url, slackreport.json, adaptivecard.json, imNotification function) with the nf-slack plugin. The plugin is declared entirely within the CI workflow's nextflow_config block, keeping local runs completely unaffected. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

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

This change needs to happen upstream in nf-core/modules, not here. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Co-authored-by: nf-core-bot <core@nf-co.re>

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

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> Co-authored-by: mashehu <mashehu3@gmail.com>

* Update conda-incubator/setup-miniconda action to v4 * [automated] Update CHANGELOG.md --------- Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: nf-core-bot <core@nf-co.re>

* Update actions/upload-artifact digest to 043fb46 * [automated] Update CHANGELOG.md --------- Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

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

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

* Update python:3.14-slim Docker digest to 5b3879b * [automated] Update CHANGELOG.md --------- Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: nf-core-bot <core@nf-co.re>

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

…5cf3 (#4220) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

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

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

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

…4223) Co-authored-by: nf-core-bot <core@nf-co.re>

…support to older pipelines

Co-authored-by: BillionClaw <billionclaw+clawoss@users.noreply.github.com> Co-authored-by: mashehu <mashehu3@gmail.com> Co-authored-by: nf-core-bot <core@nf-co.re>

codecov · 2026-04-27T13:34:26Z

Codecov Report

❌ Patch coverage is 75.35322% with 314 lines in your changes missing coverage. Please review.
✅ Project coverage is 78.37%. Comparing base (e535731) to head (37394a9).
⚠️ Report is 543 commits behind head on main.

Files with missing lines	Patch %	Lines
nf_core/pipelines/lint_utils.py	40.47%	25 Missing ⚠️
nf_core/pipelines/rocrate.py	86.02%	19 Missing ⚠️
nf_core/pipelines/download/workflow_repo.py	37.93%	18 Missing ⚠️
nf_core/modules/modules_json.py	59.52%	17 Missing ⚠️
nf_core/pipelines/schema.py	48.48%	17 Missing ⚠️
nf_core/pipelines/download/singularity.py	62.50%	15 Missing ⚠️
nf_core/components/update.py	58.82%	14 Missing ⚠️
nf_core/components/components_test.py	40.90%	13 Missing ⚠️
nf_core/__main__.py	82.60%	12 Missing ⚠️
nf_core/synced_repo.py	31.25%	11 Missing ⚠️
... and 43 more

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

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

prototaxites and others added 30 commits February 6, 2026 17:27

Update .pre-commit-config.yaml

0ccad40

Typo

2290c70

Update dawidd6/action-download-artifact action to v14 (#4018)

04c00cb

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

Update pre-commit hook astral-sh/uv-pre-commit to v0.10.2

142e0a8

[automated] Update CHANGELOG.md

4f09d59

update test to new upstream subworkflow structure

5b675f4

[automated] Update CHANGELOG.md

f99ed56

Update apptainer setup action version (#4036)

baf9e88

Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

Update GitHub Actions (#4001)

c74f6ad

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

Update mcr.microsoft.com/devcontainers/base Docker tag to v2.1.6

bb9d2d5

always have a main: section

bf2b1b2

[automated] Update CHANGELOG.md

eda1afb

add placeholder if no modules were added to pass strict syntax

ae496e3

Update dependency prettier to v3.8.1

5363b4f

Update dependency prettier to v3.8.1

08f23b4

[automated] Update CHANGELOG.md

abbc5d8

# Conflicts: # CHANGELOG.md

update all instances of prettier to 3.8.1

30b0568

set uv version to avoid api limits

77e43b4

Lock file maintenance (#4044)

2659f12

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

Lock file maintenance (#4045)

d412651

* Lock file maintenance * [automated] Update CHANGELOG.md --------- Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: nf-core-bot <core@nf-co.re>

These warnings can be ignored if the subworkflow is using topic channel

d5785ae

Update actions/stale digest to b5d41d4 (#4047)

5479929

* Update actions/stale digest to b5d41d4 * [automated] Update CHANGELOG.md --------- Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: nf-core-bot <core@nf-co.re>

Merge pull request #4046 from nf-core/topic_version_warnings

7389050

Topic version warnings

Update dawidd6/action-download-artifact action to v15 (#4053)

4ab7156

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

Revert imNotification removal from nf-core subworkflow

d984c91

This change needs to happen upstream in nf-core/modules, not here. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Merge branch 'dev' into nf-slack-bot

3008b20

hinder renovate from updating packages with a fixed range (#4058)

215b9f1

Co-authored-by: nf-core-bot <core@nf-co.re>

renovate Bot and others added 22 commits April 24, 2026 10:11

Update astral-sh/setup-uv action to v8 (#4207)

be0a1b2

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

Command to generate pipeline container config files (#3955)

7744f96

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> Co-authored-by: mashehu <mashehu3@gmail.com>

Update conda-incubator/setup-miniconda action to v4 (#4215)

237a1f0

* Update conda-incubator/setup-miniconda action to v4 * [automated] Update CHANGELOG.md --------- Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: nf-core-bot <core@nf-co.re>

Update dependency textual to v8.2.4 (#4217)

778786f

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

Update pre-commit hooks (#4219)

21eb7af

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

Update python:3.14-slim Docker digest to 5b3879b (#4221)

db6a47a

* Update python:3.14-slim Docker digest to 5b3879b * [automated] Update CHANGELOG.md --------- Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: nf-core-bot <core@nf-co.re>

Update mcr.microsoft.com/devcontainers/base Docker tag to v2.1.8 (#4218)

adad48c

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

Update mcr.microsoft.com/devcontainers/miniconda Docker digest to 1a8…

c40e895

…5cf3 (#4220) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

Update GitHub Actions (#4222)

fbc88e5

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

Download: Fix missing --outdir parameter for older pipelines.

7e5b74d

Download: Implement additional params.yml for nextflow inspect.

c76178d

Download: Adapt tests.

3dcdd53

Changelog.

d1da4a0

[automated] Update CHANGELOG.md

ac5f3ad

Apply suggestions from code review

b353644

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

Update dependency prettier to v3.8.3 (#4192)

e1025ff

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

Lock file maintenance (#4198)

5da6094

automatically handle merge conflicts for changelog files with union (#…

54ed4b1

…4223) Co-authored-by: nf-core-bot <core@nf-co.re>

Add --outdir parameter fallback to extend container image download …

f4f8566

…support to older pipelines

fix(lint): use correct config key zenodo_doi (#4201)

a79b66f

Co-authored-by: BillionClaw <billionclaw+clawoss@users.noreply.github.com> Co-authored-by: mashehu <mashehu3@gmail.com> Co-authored-by: nf-core-bot <core@nf-co.re>

bump to 4.0.0 and fix changelog (#4224)

82141d5

JulianFlesch approved these changes Apr 27, 2026

View reviewed changes

mashehu and others added 5 commits April 27, 2026 16:33

add missing nextflow setup step

e66ecde

remove todo statement from awsfulltest slack channel config (#4228)

e466c50

Update pre-commit hook astral-sh/uv-pre-commit to v0.11.8 (#4229)

bf53b29

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

Lock file maintenance (#4230)

a486c93

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

fix incorrect handling of Assertion failure for no_prompt mode (#4232)

37394a9

mashehu merged commit ba4cf6a into main Apr 28, 2026
303 of 304 checks passed

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

`dev` to `main` for 4.0.0#4225

`dev` to `main` for 4.0.0#4225
mashehu merged 272 commits into
mainfrom
dev

mashehu commented Apr 27, 2026

Uh oh!

codecov Bot commented Apr 27, 2026 •

edited

Loading

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

18 participants

Conversation

mashehu commented Apr 27, 2026

Uh oh!

codecov Bot commented Apr 27, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Codecov Report

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

18 participants

codecov Bot commented Apr 27, 2026 •

edited

Loading