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Pull requests: nf-core/tools

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Pull requests list

Add --help-json flag for machine-readable CLI help
#4310 opened May 29, 2026 by ewels Member Loading…
1
Fix dead link
#4307 opened May 28, 2026 by Aratz Contributor Loading…
3 tasks done
@Aratz
1
Update docker/setup-qemu-action digest to 0611638
#4306 opened May 28, 2026 by renovate Bot Loading…
1 task
2
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
Update pre-commit hooks
#4298 opened May 25, 2026 by renovate Bot Loading…
1 task
1
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
parse container registries from .nf-core.yml
#4282 opened May 12, 2026 by mashehu Contributor Loading…
5
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
switch to json format for nextflow inspect
#4271 opened May 7, 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
19
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
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