Skip to content

dev -> main for 4.1.0 - #4429

Merged
mashehu merged 167 commits into
mainfrom
dev
Jul 29, 2026
Merged

dev -> main for 4.1.0#4429
mashehu merged 167 commits into
mainfrom
dev

Conversation

@mashehu

@mashehu mashehu commented Jul 29, 2026

Copy link
Copy Markdown
Contributor

No description provided.

LouisLeNezet and others added 30 commits April 28, 2026 21:04
@LouisLeNezet
Fix meta comment
815ae53
@LouisLeNezet
Update changelog
8316b6e
@LouisLeNezet
Provide script to obtain EDAM
c00bc7e
@LouisLeNezet
Add edam_load test
db12b9c
@LouisLeNezet
Merge branch 'dev' into fix_meta_comments
672d19d
@LouisLeNezet
Fix linting
bc83998
@LouisLeNezet
Fix test
a8d97d0
@LouisLeNezet
Fix changelog
fd06451
@LouisLeNezet
Remove unecessary
952bbe3
@LouisLeNezet
Use NFCORE_CACHE_DIR
c5f2f29
@LouisLeNezet @mashehu
Update nf_core/modules/modules_utils.py
f3518dd 
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
@LouisLeNezet
Use TTL for EDAM.tsv
27e4706
@LouisLeNezet
Fix lint
c602f0c
@LouisLeNezet
Fix edam columns
303cd48
@mashehu
bump to 4.0.2dev
670f46b
@mashehu
Merge pull request #4249 from mashehu/bump-to-4.0.2dev
c7f861f
@mashehu
fix version capture in downloads_action
c78f901
@mashehu
add pipeline_dir to search directories for include statements
56d179b
@mashehu
downgrade logging of missing container for now
c0999d1
@mashehu
add checkout step
c1160e4
@nvnieuwk
Remove format constraint for igenomes_base
cb85e5a
@mashehu
Merge pull request #4252 from mashehu/add-main-nf-parsing
816ff24
@mashehu
Merge pull request #4253 from nf-core/nvnieuwk-patch-1
59313e5
@mashehu
Merge pull request #4251 from mashehu/fix-download-action
5f1a7b9
@mashehu
update env syntax in tools dockerfile (#4248)
b61c81e
@mashehu
bump to 4.0.2 (#4254)
9ac9191
@mashehu
bump to 4.1.0dev (#4259)
fd7903d
@renovate
Update github/branch-deploy action to v11.1.4 (#4258)
7eb2728 
Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
@pinin4fjords
docs: fix two typos in pipeline CONTRIBUTING.md (focussed -> focused,…
22fcbbc 
… duplicate 'the')

Both typos in nf_core/pipeline-template/docs/CONTRIBUTING.md ship with
every pipeline that adopts the 4.0 template. 'focussed' is a less-common
British spelling; 'focused' is preferred in modern AmE and BrE style
guides. The second hit (line 54) is a duplicated 'the the'.

Caught downstream during the nf-core/rnaseq#1827 template merge review.
@pinin4fjords
chore: trigger CI after base branch update
59d428e
renovate Bot and others added 24 commits July 20, 2026 10:51
@renovate
Update j178/prek-action digest to 5337cb9 (#4399)
f0eb0e2 
Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
@renovate
Update dependency prettier to v3.9.5 (#4400)
bdaacf3
@renovate
Update mcr.microsoft.com/devcontainers/miniconda Docker digest to 617…
6752f5d 
…c7e4 (#4402)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
@renovate
Update python:3.14-slim Docker digest to cea0e60 (#4403)
3afcd03 
Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
@renovate
Update dependency prettier to v3.9.6 (#4405)
d17c641
@renovate
Update GitHub Actions (#4404)
e48481b 
Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
@renovate
Update actions/setup-python action to v7 (#4401)
6d01b86 
Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
@renovate @mashehu
Update pre-commit hooks (#4359)
cb0ac11 
Co-authored-by: mashehu <mashehu3@gmail.com>
@renovate @mashehu
Update dependency textual to v8.2.7 (#4256)
b03c230 
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
@renovate
Update nf-core/setup-nextflow digest to 893c28b (#4407)
8724e1d 
Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
@renovate
Update astral-sh/setup-uv action to v9 (#4408)
f79d71c 
Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
@renovate
Update docker/login-action digest to 06fb636 (#4417)
e2faa41 
Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
@renovate
Update github/branch-deploy action to v12 (#4418)
8190b08 
Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
@mashehu
Merge remote-tracking branch 'upstream/main' into backmerge-4.0.3
3acb08c
@renovate
Update docker/login-action digest to 371161b (#4421)
97044e9 
Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
@renovate
Update dependency setuptools to v83 [SECURITY] (#4413)
3c84e83
@renovate
Update pre-commit hooks (#4424)
be3afc3
@renovate
Update mcr.microsoft.com/devcontainers/base Docker tag to v2.1.11 (#4423
2c0bf87 
)
@renovate
Update dependency textual to v8.2.8 (#4422)
87320d9
@mashehu
add nextflow version fallback to sync action (#4425)
d809a90
@mashehu
fix changelog action (#4426)
491ab83
@mashehu
bump to 4.1.0 and update components in template (#4398)
efb1a47
@renovate
Update CodSpeedHQ/action action to v5 (#4428)
7dc6cb4 
Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
@renovate
Update docker/login-action digest to dbcb813 (#4427)
8459516 
Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
@codecov

codecov Bot commented Jul 29, 2026 •
edited
Loading

Copy link
Copy Markdown

Codecov Report

❌ Patch coverage is 77.38802% with 419 lines in your changes missing coverage. Please review.
✅ Project coverage is 78.29%. Comparing base (ae4951a) to head (cb623e0).
⚠️ Report is 1 commits behind head on main.

Files with missing lines Patch % Lines
nf_core/modules/containers.py 77.99% 103 Missing ⚠️
nf_core/__main__.py 45.74% 51 Missing ⚠️
nf_core/commands_modules.py 0.00% 49 Missing ⚠️
nf_core/modules/lint/module_containers.py 71.20% 36 Missing ⚠️
nf_core/modules/modules_utils.py 77.06% 25 Missing ⚠️
nf_core/github_api.py 79.64% 23 Missing ⚠️
nf_core/pipelines/download/singularity.py 66.15% 22 Missing ⚠️
nf_core/components/nfcore_component.py 67.24% 19 Missing ⚠️
nf_core/modules/bump_versions.py 82.02% 16 Missing ⚠️
nf_core/modules/lint/environment_yml.py 82.25% 11 Missing ⚠️
... and 21 more

☔ View full report in Codecov by Harness.
📢 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.

@mashehu
mashehu merged commit eb2f709 into main Jul 29, 2026
217 of 218 checks passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

@JulianFlesch JulianFlesch JulianFlesch approved these changes

Assignees

No one assigned

Labels

None yet

Projects

None yet

Milestone

No milestone

Development

Successfully merging this pull request may close these issues.