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Redesign input system and clean up repository for nf-core compliance #1

	name: nf-test
	on:
	push:
	branches: [main, dev, 'nf-core/**']
	pull_request:
	branches: [main, dev]
	workflow_dispatch:

	concurrency:
	group: "${{ github.workflow }}-${{ github.event.pull_request.number \|\| github.ref }}"
	cancel-in-progress: true

	jobs:
	changes:
	name: Check changes
	runs-on: ubuntu-latest
	outputs:
	nf_test_files: ${{ steps.list.outputs.components }}
	has_changes: ${{ steps.list.outputs.has_changes }}
	steps:
	- uses: actions/checkout@v4
	- name: List nf-test files
	id: list
	uses: ./.github/actions/get-shards

	test:
	name: "Test ${{ matrix.shard }}"
	needs: changes
	if: needs.changes.outputs.has_changes == 'true'
	runs-on: ubuntu-latest
	strategy:
	fail-fast: false
	matrix:
	shard: ${{ fromJson(needs.changes.outputs.nf_test_files) }}
	profile: [docker]
	NXF_VER:
	- "24.04.2"
	- "latest-everything"
	steps:
	- uses: actions/checkout@v4
	- uses: ./.github/actions/nf-test
	with:
	shard: ${{ matrix.shard }}
	profile: ${{ matrix.profile }}
	nextflow_version: ${{ matrix.NXF_VER }}

	confirm:
	name: nf-test-success
	if: always()
	needs: [changes, test]
	runs-on: ubuntu-latest
	steps:
	- name: All tests passed
	if: needs.test.result == 'success' \|\| needs.changes.outputs.has_changes != 'true'
	run: echo "All tests passed"
	- name: Some tests failed
	if: needs.test.result != 'success' && needs.changes.outputs.has_changes == 'true'
	run: exit 1