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Pull requests: nf-core/tools

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Pull requests list

pipelines bump-version: fix indentation for list in dumped .nf-core.yml
#3829 opened Oct 14, 2025 by mashehu Loading…
1
feat: Add codespaces badge to template README
#3824 opened Oct 14, 2025 by JulianFlesch Loading…
4 tasks
@JulianFlesch
1
Improve file ignores in workflow file enumeration
#3820 opened Oct 8, 2025 by jmuhlich • Draft
1 of 4 tasks
1
3
TEMPLATE: add a fallback for new outputdir parameter
#3798 opened Oct 3, 2025 by mashehu Loading… 3.5.0
2
Migrate template to nf-core-utils plugin
#3790 opened Oct 1, 2025 by edmundmiller Loading…
4 tasks
5
Add topics to the template + update linting
#3779 opened Sep 26, 2025 by nvnieuwk Loading…
4 tasks
2
feat: Add Claude Code hooks for automated testing and linting
#3774 opened Sep 25, 2025 by edmundmiller • Draft
4 tasks done
3.5.0
@edmundmiller
3
Testing out Reftrace for regex replacement in modules
#3745 opened Sep 2, 2025 by ningyuxin1999 • Draft
4 tasks
3.5.0
@ningyuxin1999
4
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…
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
Automatically sync the Rocrate and README content during pipelines lint
#3688 opened Jul 28, 2025 by ningyuxin1999 Loading…
4 tasks
14
Lint for version captures in modules
#3676 opened Jul 11, 2025 by edmundmiller Loading…
4 tasks
3.5.0
@edmundmiller
27
Fix collectFile cache issue causing software version inconsistencies
#3654 opened Jul 2, 2025 by ewels • Draft
2 of 4 tasks
1
@ewels
11
linting: fix type error when linting modules.json
#3611 opened Jun 11, 2025 by mashehu Loading…
1
Download pipelines with authenticated GH API calls
#3607 opened Jun 5, 2025 by jpfeuffer Loading…
1 of 4 tasks
3.5.0
@JulianFlesch
32
Document ext.args in meta yml
#3451 opened Feb 12, 2025 by awgymer Loading…
4 tasks
1
13
create template GENERATE_DOWNSTREAM_SAMPLESHEETS for tools
#3261 opened Oct 29, 2024 by Joon-Klaps • Draft
4 tasks
3.5.0
11
Create pre-commit hooks
#3141 opened Aug 26, 2024 by edmundmiller Loading…
@edmundmiller
7
Adopt pyproject.toml
#3139 opened Aug 26, 2024 by edmundmiller • Draft
@edmundmiller
3
Support version topic channels
#3093 opened Aug 1, 2024 by edmundmiller Loading…
4 tasks
@edmundmiller
5
fix the nested list bug that makes email not be delivered
#3081 opened Jul 25, 2024 by HaidYi Loading…
2 of 4 tasks
12
Add nf-core configs create sub command (attempt 2)
#3001 opened May 25, 2024 by jfy133 • Draft
1 of 9 tasks
3.5.0
1
5
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