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Pull requests: nf-core/tools

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Pull requests list

Add more ruff rules (B, PTH, RSE, SIM, C4, BLE)
#4034 opened Feb 11, 2026 by mashehu Loading…
4 of 10 tasks
1
Fix incompatible Docker Daemon Version in Devcontainer
#4029 opened Feb 4, 2026 by JulianFlesch • Draft
4 tasks
1
TEMPLATE: Add bioconda channel to conda setup
#3987 opened Jan 19, 2026 by maxulysse Loading…
4 tasks
4
Escape original merge branch to compile regex
#3984 opened Jan 16, 2026 by rrahn 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
Add aliases to sub-subcommands like install, lint, etc.
#3980 opened Jan 12, 2026 by mashehu Loading…
2
split subworkflow/test_lint into separate files
#3965 opened Dec 10, 2025 by mashehu Loading…
1
Command to generate pipeline container config files
#3955 opened Dec 2, 2025 by mirpedrol Loading…
2 of 5 tasks
18
Implement wave container commands
#3954 opened Dec 2, 2025 by JulianFlesch • Draft
2 of 4 tasks
@ningyuxin1999
29
Configbuilder: nf-core configs create
#3949 opened Dec 1, 2025 by mirpedrol Loading…
1
1
sync: don't overwrite the defaultBranch if already set in nextflow.config
#3939 opened Nov 27, 2025 by mashehu Loading…
1
Pipeline template: New pre-commit hooks (large files, merge conflicts)
#3935 opened Nov 26, 2025 by MatthiasZepper Loading…
2 of 4 tasks
17
feat(template): trigger nf-test full run if scripts in bin modified
#3897 opened Nov 13, 2025 by prototaxites Loading…
2 of 4 tasks
3.6.0
4
simplify TEMPLATE with nf-core-utils 0.4.0
#3870 opened Nov 4, 2025 by maxulysse Loading…
4 tasks
4
TEMPLATE: add a fallback for new outputdir parameter
#3798 opened Oct 3, 2025 by mashehu Loading…
2
Migrate template to nf-core-utils plugin
#3790 opened Oct 1, 2025 by edmundmiller • Draft
4 tasks
@adamrtalbot
15
Testing out Reftrace for regex replacement in modules
#3745 opened Sep 2, 2025 by ningyuxin1999 • Draft
4 tasks
3.5.0
@ningyuxin1999
5
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… 3.6.0
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
Lint for version captures in modules
#3676 opened Jul 11, 2025 by edmundmiller Loading…
4 tasks
@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
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