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Pull requests: nf-core/tools

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Pull requests list

Enable Slack notifications on pipeline start for megatests
#4349 opened Jun 25, 2026 by maxulysse Member Loading…
4 tasks
1
Template: Fix publishDir configuration in modules.config for multiqc
#4347 opened Jun 24, 2026 by maxulysse Member Loading…
4 tasks
4
fix: allow dots in usernames for non-GitHub git providers
#4343 opened Jun 24, 2026 by sanmaxdev Loading…
4 tasks done
2
switch to more secure split PR comment approach
#4342 opened Jun 23, 2026 by mashehu Contributor Loading…
1
test: cover val substring in emit names
#4340 opened Jun 22, 2026 by joeydufourd Loading…
2 of 4 tasks
4
Bump msgpack from 1.1.2 to 1.2.1 dependencies Pull requests that update a dependency file python:uv Pull requests that update python:uv code
#4339 opened Jun 19, 2026 by dependabot Bot Loading…
1
Update GitHub Actions (major)
#4338 opened Jun 19, 2026 by renovate Bot Loading…
1 task
1
Update GitHub Actions
#4332 opened Jun 17, 2026 by renovate Bot Loading…
1 task
2
Bump aiohttp from 3.13.5 to 3.14.1 dependencies Pull requests that update a dependency file python:uv Pull requests that update python:uv code
#4330 opened Jun 17, 2026 by dependabot Bot Loading…
1
Bump cryptography from 47.0.0 to 48.0.1 dependencies Pull requests that update a dependency file python:uv Pull requests that update python:uv code
#4329 opened Jun 17, 2026 by dependabot Bot Loading…
1
Bump pyjwt from 2.12.1 to 2.13.0 dependencies Pull requests that update a dependency file python:uv Pull requests that update python:uv code
#4326 opened Jun 16, 2026 by dependabot Bot Loading…
1
fix: correct always-true lint condition and template doc typos
#4324 opened Jun 12, 2026 by znorgaard Loading…
3 of 4 tasks
1
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 • Draft
2 of 4 tasks
@muffato @mashehu
5
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…
3
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
ProTip! What’s not been updated in a month: updated:<2026-05-25.