Merge pull request #116 from kbestak/test_updates

Use nf-test in CI

Author: kbestak

.github/workflows/ci.yml

@@ -10,6 +10,7 @@ on:
   workflow_dispatch:
 
 env:
+  NFT_VER: "0.9.0"
   NXF_ANSI_LOG: false
   NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
   NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
@@ -19,18 +20,41 @@ concurrency:
   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/detect-nf-test-changes@v0.0.4
+        with:
+          head: ${{ github.sha }}
+          base: ${{ github.event.pull_request.base.sha || github.event.merge_group.base_sha || github.event.before }}
+
+      - name: print list of nf-test files
+        run: |
+          echo ${{ steps.list.outputs.components }}
+
   test:
-    name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }})"
+    name: "Run tests (${{ matrix.nf_test_files }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }})"
     # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/molkart') }}"
+    needs: [nf-test-changes]
+    if: "${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/molkart')) && needs.nf-test-changes.outputs.nf_test_files != '[]' }}"
     runs-on: ubuntu-latest
     strategy:
       matrix:
         NXF_VER:
           - "24.04.2"
           - "latest-everything"
+        nf_test_files: ["${{ fromJson(needs.nf-test-changes.outputs.nf_test_files) }}"]
         profile:
-          - "conda"
           - "docker"
           - "singularity"
         test_name:
@@ -41,12 +65,15 @@ jobs:
           - profile: "conda"
 
     steps:
+      - name: install curl
+        run: sudo apt update && sudo apt install -y curl
+
       - name: Check out pipeline code
         uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         with:
           fetch-depth: 0
 
-      - name: Set up Nextflow
+      - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
         with:
           version: "${{ matrix.NXF_VER }}"
@@ -61,9 +88,63 @@ jobs:
           mkdir -p $NXF_SINGULARITY_CACHEDIR
           mkdir -p $NXF_SINGULARITY_LIBRARYDIR
 
+      - name: Install nf-test
+        uses: nf-core/setup-nf-test@v1
+        with:
+          version: ${{ env.NFT_VER }}
+
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+          architecture: "x64"
+
+      - name: Install pdiff to see diff between nf-test snapshots
+        run: |
+          python -m pip install --upgrade pip
+          pip install pdiff
+
       - name: Clean up Disk space
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}"
+      - name: Run nf-test
+        run: |
+          nf-test test \
+            --verbose ${{ matrix.nf_test_files }} \
+            --profile "+${{ matrix.profile }},test" \
+            --junitxml=test.xml \
+            --tap=test.tap
+
+      - uses: pcolby/tap-summary@v1
+        with:
+          path: >-
+            test.tap
+
+      - name: Output log on failure
+        if: failure()
+        run: |
+          sudo apt install bat > /dev/null
+          batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/meta/nextflow.log
+
+      - name: Publish Test Report
+        uses: mikepenz/action-junit-report@v3
+        if: always()
+        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: |
-          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results
+          echo "toJSON(needs) = ${{ toJSON(needs) }}"
+          echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"

CHANGELOG.md

@@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Changed
 
 - [PR #111](https://github.com/nf-core/molkart/pull/111) - Updated json schemas (@kbestak)
+- [PR #116](https://github.com/nf-core/molkart/pull/116) - Update CI to use nf-test on changed files (@kbestak)
 
 ### Fixed
 

modules.json

@@ -27,17 +27,17 @@
                     },
                     "mindagap/duplicatefinder": {
                         "branch": "master",
-                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
+                        "git_sha": "a84e5d699986fac96d7d7f01044a339a343af827",
                         "installed_by": ["modules"]
                     },
                     "mindagap/mindagap": {
                         "branch": "master",
-                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
+                        "git_sha": "a84e5d699986fac96d7d7f01044a339a343af827",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
+                        "git_sha": "7b50cb7be890e4b28cffb82e438cc6a8d7805d3f",
                         "installed_by": ["modules"]
                     },
                     "stardist": {