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Pull requests: nf-core/tools

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Pull requests list

Bump cryptography from 46.0.4 to 46.0.7 dependencies Pull requests that update a dependency file python:uv Pull requests that update python:uv code
#4181 opened Apr 8, 2026 by dependabot bot Loading…
Fix: Issue #4173 awaiting-changes Needs changes after a review. Remove label when ready to be reviewed again. awaiting-feedback
#4174 opened Apr 4, 2026 by sonusonukgupta-gif Loading…
1
Bump aiohttp from 3.13.3 to 3.13.4 dependencies Pull requests that update a dependency file python:uv Pull requests that update python:uv code
#4168 opened Apr 1, 2026 by dependabot bot Loading…
1
Remove --migrate-pytest functionality and deprecated pipeline commands
#4167 opened Apr 1, 2026 by JulianFlesch Contributor Loading…
4 tasks
4.0.0
2
[DO NOT MERGE] test esm version of setup-nf-test [skip changelog]
#4164 opened Apr 1, 2026 by mashehu Contributor Loading…
2
linting: make version topics mandatory
#4163 opened Apr 1, 2026 by mashehu Contributor Loading… 4.0.0
1
Update dependency setuptools to v82
#4154 opened Mar 31, 2026 by renovate bot Loading…
1 task
1
Bump pygments from 2.19.2 to 2.20.0 dependencies Pull requests that update a dependency file python:uv Pull requests that update python:uv code
#4149 opened Mar 30, 2026 by dependabot bot Loading…
1
Parse manifest.contributors to fill in the RO-Crate
#4147 opened Mar 29, 2026 by muffato Member Loading…
2 of 4 tasks
4.1.0
@muffato
9
Request org details to fill in more template fields
#4146 opened Mar 29, 2026 by muffato Member • Draft
4 tasks
4.1.0
@muffato
12
Bump requests from 2.32.5 to 2.33.0 dependencies Pull requests that update a dependency file python:uv Pull requests that update python:uv code
#4136 opened Mar 26, 2026 by dependabot bot Loading…
1
Replace all links in pipeline template to upcoming docs-v2 overhaul equivalents
#4135 opened Mar 25, 2026 by jfy133 Member Loading…
4 tasks
4.0.0
15
Add TTY detection to prevent CLI hanging in non-interactive sessions
#4130 opened Mar 23, 2026 by ewels Member Loading…
5 tasks
4.0.0
17
Bump pyjwt from 2.10.1 to 2.12.0 dependencies Pull requests that update a dependency file python:uv Pull requests that update python:uv code
#4120 opened Mar 14, 2026 by dependabot bot Loading…
1
added "auto process" screen and extracted labels/names from nf
#4117 opened Mar 13, 2026 by imkhoibui Loading…
4 tasks
1
template: workflow output for multiQC
#4093 opened Mar 6, 2026 by maxulysse Member Loading…
4 tasks
5.0.0
4
linting: lint for correct syntax for compressed files in stubs
#4048 opened Feb 17, 2026 by mashehu Contributor Loading… 4.0.0
3
Add more ruff rules (B, PTH, RSE, SIM, C4, BLE, A)
#4034 opened Feb 11, 2026 by mashehu Contributor Loading…
5 tasks done
4.0.0
8
Fix incompatible Docker Daemon Version in Devcontainer
#4029 opened Feb 4, 2026 by JulianFlesch Contributor • Draft
4 tasks
1
TEMPLATE: Add bioconda channel to conda setup
#3987 opened Jan 19, 2026 by maxulysse Member Loading…
4 tasks
4
Escape original merge branch to compile regex
#3984 opened Jan 16, 2026 by rrahn Contributor Loading…
3 of 4 tasks
1
added helpful comment for common gotcha - prefix scoping
#3982 opened Jan 15, 2026 by ammaraziz Loading…
1 of 2 tasks
1
split subworkflow/test_lint into separate files
#3965 opened Dec 10, 2025 by mashehu Contributor Loading… 4.0.0
2
Command to generate pipeline container config files
#3955 opened Dec 2, 2025 by mirpedrol Member Loading…
2 of 5 tasks
4.0.0
18
Implement wave container commands
#3954 opened Dec 2, 2025 by JulianFlesch Contributor • Draft
4 tasks done
4.1.0
@ningyuxin1999
40
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