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Pull requests: nf-core/tools

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Pull requests list

fix wrong parsing when output values contain spaces
#3999 opened Jan 29, 2026 by mirpedrol Loading…
1
use shared function for plain text linting in modules and piplines
#3996 opened Jan 26, 2026 by mashehu Loading…
1
Add plain-text output option to lint commands
#3993 opened Jan 26, 2026 by ewels Loading…
4 tasks
9
handle type for val in topics correctly
#3991 opened Jan 21, 2026 by mashehu Loading…
7
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
configbuilder: add pipeline config screens, fix validation code
#3974 opened Dec 18, 2025 by mgeaghan Loading…
1 of 4 tasks
12
Subworkflow lint bugfixes
#3968 opened Dec 10, 2025 by andresferben Loading…
3 of 4 tasks
3.5.2
9
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
1 of 4 tasks
@ningyuxin1999
29
Configbuilder: nf-core configs create
#3949 opened Dec 1, 2025 by mirpedrol Loading…
Update dependency prettier to v3.7.3
#3944 opened Dec 1, 2025 by renovate bot Loading…
1 task
1
Update pre-commit hook astral-sh/ruff-pre-commit to v0.14.7
#3943 opened Dec 1, 2025 by renovate bot Loading…
1 task
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
Update python:3.14-slim Docker digest to 119fd5b
#3910 opened Nov 19, 2025 by renovate bot Loading…
1 task
4
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
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