#1124 FEAT: Replace pre-commit with prek Pull request opened by maxulysse Description Replace pre-commit with prek. prek is fully compatible with the existing

.pre-commit-config.yaml

— no config changes needed. Changes

.github/workflows/linting.yml

• Replaced

pre-commit/action@v3.0.1

(which required Python +

actions/setup-python

) with direct prek installation • prek is installed via a single curl command and run with

prek run --all-files

.github/workflows/fix-linting.yml

• Removed

actions/setup-python

and

pip install pre-commit

• Replaced with

curl ... | sh

for prek and

prek run --all-files

• Updated step id references from

pre-commit

to

prek

All logic is coming from the modules repo nf-core/configs