CI: try nf-test shard from nascent

.github/include.yaml

@@ -0,0 +1,10 @@
+".":
+  - ./.github/workflows/**
+  - ./nf-test.config
+  - ./nextflow.config
+tests:
+  - ./assets/*
+  - ./bin/*
+  - ./conf/*
+  - ./main.nf
+  - ./nextflow_schema.json

.github/workflows/ci.yml

@@ -1,7 +1,12 @@
 name: nf-core CI
 # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
 on:
+  push:
+    branches:
+      - dev
   pull_request:
+  release:
+    types: [published]
 
 env:
   NXF_ANSI_LOG: false
@@ -13,52 +18,21 @@ env:
 concurrency:
   group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
   cancel-in-progress: true
-jobs:
-  nf-test-changes:
-    name: Check for changes
-    runs-on: ubuntu-latest
-    outputs:
-      nf_test_files: ${{ steps.list.outputs.components }}
-    steps:
-      - uses: actions/checkout@v4
-        with:
-          fetch-depth: 0
-
-      - name: List nf-test files
-        id: list
-        uses: adamrtalbot/[email protected]
-        with:
-          head: ${{ github.sha }}
-          base: origin/${{ github.base_ref }}
-          include: .github/include.yaml
-
-      - name: print list of nf-test files
-        run: |
-          echo ${{ steps.list.outputs.components }}
 
+jobs:
   test:
-    name: ${{ matrix.nf_test_files }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }}
-    needs: [nf-test-changes]
-    if: needs.nf-test-changes.outputs.nf_test_files != '[]'
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        NXF_VER:
-          - "latest-everything"
-          - "23.04"
-        nf_test_files: ["${{ fromJson(needs.nf-test-changes.outputs.nf_test_files) }}"]
-        profile:
-          - "docker"
-
+        shard: [1, 2, 3, 4]
+        NXF_VER: ["latest-stable"] # TODO Test minimum version on release
+        profile: ["docker"]
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
-
-      - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v2
         with:
-          version: "${{ matrix.NXF_VER }}"
+          fetch-depth: 0
 
       - uses: actions/setup-python@v4
         with:
@@ -70,43 +44,25 @@ jobs:
           python -m pip install --upgrade pip
           pip install pdiff
 
-      - uses: nf-core/setup-nf-test@v1
-
-      - name: Run nf-test
-        run: |
-          nf-test test --verbose ${{ matrix.nf_test_files }} --profile "+${{ matrix.profile }}" --junitxml=test.xml --tap=test.tap
+      - uses: nf-core/setup-nextflow@v2
+        with:
+          version: "${{ matrix.NXF_VER }}"
 
-      - uses: pcolby/tap-summary@v1
+      - uses: nf-core/setup-nf-test@v1
         with:
-          path: >-
-            test.tap
+          version: ${{ env.NFT_VER }}
 
-      - name: Output log on failure
-        if: failure()
+      - name: Run Tests (Shard ${{ matrix.shard }}/${{ strategy.job-total }})
         run: |
-          sudo apt install bat > /dev/null
-          batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/meta/nextflow.log
+          nf-test test \
+              --ci \
+              --shard ${{ matrix.shard }}/${{ strategy.job-total }} \
+              --changed-since HEAD^ \
+              --profile "+${{ matrix.profile }}" \
+              --filter pipeline
 
       - name: Publish Test Report
         uses: mikepenz/action-junit-report@v3
         if: always() # always run even if the previous step fails
         with:
           report_paths: test.xml
-
-  confirm-pass:
-    runs-on: ubuntu-latest
-    needs: [test]
-    if: always()
-    steps:
-      - name: All tests ok
-        if: ${{ !contains(needs.*.result, 'failure') }}
-        run: exit 0
-      - name: One or more tests failed
-        if: ${{ contains(needs.*.result, 'failure') }}
-        run: exit 1
-
-      - name: debug-print
-        if: always()
-        run: |
-          echo "toJSON(needs) = ${{ toJSON(needs) }}"
-          echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"