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Pull requests: nf-core/tools

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Pull requests list

fix: relax stub .gz linting regex to accept echo without arguments
#4323 opened Jun 11, 2026 by handsomesix Loading…
1
1
Add AGENTS.md file and the related template feature
#4318 opened Jun 9, 2026 by itrujnara Contributor • Draft
2 of 4 tasks
9
drop ext.when in module template
#4314 opened Jun 4, 2026 by matthdsm Contributor Loading…
2 of 4 tasks
3
Bump aiohttp from 3.13.5 to 3.14.0 dependencies Pull requests that update a dependency file python:uv Pull requests that update python:uv code
#4313 opened Jun 4, 2026 by dependabot Bot Loading…
1
Add --help-json flag for machine-readable CLI help WIP Work in progress
#4310 opened May 29, 2026 by ewels Member • Draft
6
Update terminology from 'GitHub' to 'Git'
#4304 opened May 27, 2026 by ewels Member Loading…
2
Fix nextflow info -d parsing in LocalWorkflow and preserve local_path path semantics
#4302 opened May 26, 2026 by Copilot AI Loading…
@jpfeuffer
1
fix(lint): use repo-root-relative path in git restore call in container_configs
#4301 opened May 26, 2026 by Copilot AI Loading…
5 tasks done
@jpfeuffer
6
Bump idna from 3.13 to 3.15 dependencies Pull requests that update a dependency file python:uv Pull requests that update python:uv code
#4290 opened May 19, 2026 by dependabot Bot Loading…
1
Add README badge to pipeline documentation to pipeline template
#4288 opened May 19, 2026 by jfy133 Member Loading…
4 tasks
9
Simpler test data path in tests/nextflow.config
#4285 opened May 18, 2026 by maxulysse Member Loading…
4 tasks
1
Bump urllib3 from 2.6.3 to 2.7.0 dependencies Pull requests that update a dependency file python:uv Pull requests that update python:uv code
#4281 opened May 11, 2026 by dependabot Bot Loading…
1
4250 meta key linting
#4280 opened May 11, 2026 by DLBPointon Loading…
3 of 4 tasks
2
Bump gitpython from 3.1.49 to 3.1.50 dependencies Pull requests that update a dependency file python:uv Pull requests that update python:uv code
#4275 opened May 9, 2026 by dependabot Bot Loading…
1
avoid prek input overload and forward --verbose to it
#4272 opened May 8, 2026 by mashehu Contributor Loading…
1
feat(template): add axis-decomposed process_cpus_* / process_mem_* labels
#4265 opened May 6, 2026 by pinin4fjords Member Loading…
2
Lock file maintenance
#4257 opened May 1, 2026 by renovate Bot Loading…
1 task
1
Update dependency textual to v8.2.7
#4256 opened May 1, 2026 by renovate Bot Loading…
1 task
4
Fix edam comments
#4242 opened Apr 28, 2026 by LouisLeNezet Contributor Loading…
4 tasks
@LouisLeNezet
23
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
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
Fix incompatible Docker Daemon Version in Devcontainer
#4029 opened Feb 4, 2026 by JulianFlesch Contributor • Draft
4 tasks
1
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