Skip to content

Pull requests: nf-core/tools

New pull request New
42 Open 2,623 Closed
42 Open 2,623 Closed
Author
Filter by author
Loading
Label
Filter by label
Loading
Use alt + click/return to exclude labels
or ⇧ + click/return for logical OR
Projects
Filter by project
Loading
Milestones
Filter by milestone
Loading
Reviews
Filter by reviews
No reviews Review required Approved review Changes requested
Assignee
Filter by who’s assigned
Assigned to nobody Loading
Sort
Sort by
Newest Oldest Most commented Least commented Recently updated Least recently updated Best match
Most reactions
👍 👎 😄 🎉 😕 ❤️ 🚀 👀

Pull requests list

Update GitHub Actions (major)
#3971 opened Dec 13, 2025 by renovate bot Loading…
1 task
2
Update astral-sh/setup-uv action to v7.1.5
#3970 opened Dec 12, 2025 by renovate bot Loading…
1 task
2
Subworkflow lint bugfixes
#3968 opened Dec 10, 2025 by andresferben Loading…
2 of 4 tasks
1
split subworkflow/test_lint into separate files
#3965 opened Dec 10, 2025 by mashehu Loading…
[WIP] Command to generate pipeline container config files
#3955 opened Dec 2, 2025 by mirpedrol Loading…
2 of 5 tasks
9
Implement wave container commands
#3954 opened Dec 2, 2025 by JulianFlesch • Draft
4 tasks
@ningyuxin1999
26
Configbuilder: nf-core configs create
#3949 opened Dec 1, 2025 by mirpedrol Loading…
Update dependency prettier to v3.7.3
#3944 opened Dec 1, 2025 by renovate bot Loading…
1 task
1
Update pre-commit hook astral-sh/ruff-pre-commit to v0.14.7
#3943 opened Dec 1, 2025 by renovate bot Loading…
1 task
1
sync: don't overwrite the defaultBranch if already set in nextflow.config
#3939 opened Nov 27, 2025 by mashehu Loading…
1
Pipeline template: New pre-commit hooks (large files, merge conflicts)
#3935 opened Nov 26, 2025 by MatthiasZepper Loading…
2 of 4 tasks
17
Simplify coverage reporting in pytest.yml
#3934 opened Nov 26, 2025 by mashehu Loading…
1
Update python:3.14-slim Docker digest to 119fd5b
#3910 opened Nov 19, 2025 by renovate bot Loading…
1 task
4
add schema to devcontainer.json
#3908 opened Nov 18, 2025 by mashehu Loading… 3.6.0
1
Move CONTRIBUTING.md to docs/, review and update text, and add pipline-specific conventions section
#3903 opened Nov 16, 2025 by jfy133 Loading…
1 of 4 tasks
5
feat(template): trigger nf-test full run if scripts in bin modified
#3897 opened Nov 13, 2025 by prototaxites Loading…
2 of 4 tasks
3.6.0
4
simplify TEMPLATE with nf-core-utils 0.4.0
#3870 opened Nov 4, 2025 by maxulysse Loading…
4 tasks
4
TEMPLATE: add a fallback for new outputdir parameter
#3798 opened Oct 3, 2025 by mashehu Loading…
2
Migrate template to nf-core-utils plugin
#3790 opened Oct 1, 2025 by edmundmiller • Draft
4 tasks
@adamrtalbot
15
Testing out Reftrace for regex replacement in modules
#3745 opened Sep 2, 2025 by ningyuxin1999 • Draft
4 tasks
3.5.0
@ningyuxin1999
5
Use branch-deploy action
#3744 opened Sep 2, 2025 by kevinbackhouse Loading…
4 tasks
3
Tests cleanup
#3733 opened Aug 27, 2025 by edmundmiller • Draft
2
@edmundmiller
15
General: add pytest for get_wf_files
#3725 opened Aug 26, 2025 by mirpedrol Loading… 3.6.0
7
Patch patch command
#3714 opened Aug 15, 2025 by ErikDanielsson Loading…
2 of 4 tasks
@ErikDanielsson
5
TEMPLATE - add trainling slash for pipelines_testdata_base_path
#3701 opened Aug 5, 2025 by maxulysse Loading…
4 tasks
3
ProTip! Adding no:label will show everything without a label.