#1123 FEAT: Refactor CI to only test modified files Pull request opened by maxulysse Description Replace the hardcoded 154-profile test matrix with a dynamic

detect-changes

job that only tests profiles affected by the PR. Inspired by nf-core/modules' approach with

detect-nf-test-changes

. Changes

.github/workflows/main.yml

• New

detect-changes

job: Uses

git diff

with

fetch-depth: 0

between base and head to determine which files changed, then builds a JSON test matrix dynamically • Dynamic

profile_test

matrix: Instead of a hardcoded list of 154 profiles, the matrix is built from

fromJson(needs.detect-changes.outputs.tests)

• Smart test selection: • Push to master → test all profiles • Core infrastructure (main.yml, nextflow.config, nfcore_custom.config, configtest.nf, bin/) → test all profiles •

conf/<name>.config

changes → test only that profile •

conf/sanger/farm22.config

or

conf/uppmax/rackham.config

changes → test the parent profile •

conf/pipeline/<pipeline>/<name>.config

changes → test the matching pipeline profiles with

-c pipeline/<pipeline>.config --custom_config_base ${GITHUB_WORKSPACE}

• Only docs changed → skip tests entirely • Pipeline tests: New

type: pipeline

test steps that run

nextflow run <http://configtest.nf|configtest.nf> -profile <name> -c pipeline/<pipeline>.config --custom_config_base ${GITHUB_WORKSPACE}

bin/cchecker.py

• Removed GitHub Actions matrix validation (no longer a hardcoded matrix) • Now validates internal consistency: • All profiles in

nfcore_custom.config

have config files in

conf/

• All config files in

conf/

are registered in

nfcore_custom.config

• All pipeline-specific configs are referenced in

pipeline/<pipeline>.config

Testing This PR should be tested by creating a PR that modifies a single config file and verifying only that profile's test runs. nf-core/configs