Merge pull request #359 from nf-core/fix-nf-test

Fix that tests are not executed

.github/workflows/ci.yml

@@ -16,7 +16,10 @@ on:
 
 env:
   NXF_ANSI_LOG: false
-  NFTEST_VER: "0.8.1"
+  NFT_VER: "0.9.0"
+  NFT_WORKDIR: "~"
+  NFT_DIFF: "pdiff"
+  NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2"
 
 concurrency:
   group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
@@ -42,29 +45,30 @@ jobs:
       - name: Check out pipeline code
         uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
-      - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v2
+      - uses: actions/setup-python@v4
         with:
-          version: "${{ matrix.NXF_VER }}"
+          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: Cache nf-test installation
-        id: cache-software
-        uses: actions/cache@v3
+      - uses: nf-core/setup-nextflow@v2
         with:
-          path: |
-            /usr/local/bin/nf-test
-            /home/runner/.nf-test/nf-test.jar
-          key: ${{ runner.os }}-${{ env.NFTEST_VER }}-nftest
+          version: "${{ matrix.NXF_VER }}"
 
-      - name: Install nf-test
-        if: steps.cache-software.outputs.cache-hit != 'true'
-        run: |
-          wget -qO- https://code.askimed.com/install/nf-test | bash
-          sudo mv nf-test /usr/local/bin/
+      - uses: nf-core/setup-nf-test@v1
+        with:
+          version: ${{ env.NFT_VER }}
 
       - name: Run nf-test
         run: |
-          nf-test test tests/main_pipeline_${{ matrix.profile }}.test --junitxml=test.xml
+          nf-test test \
+            --ci \
+            --junitxml=test.xml \
+            tests/main_pipeline_${{ matrix.profile }}.nf.test
 
       - name: Output log on failure
         if: failure()

.nf-core.yml

@@ -6,3 +6,6 @@ lint:
     - .github/ISSUE_TEMPLATE/bug_report.yml
   files_exist:
     - lib/Utils.groovy
+  # TODO This is because of an issue with the monochromeLogs parameter
+  # See nextflow.config for details
+  schema_params: False

CHANGELOG.md

@@ -5,7 +5,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## v2.7.1 - 2024-08-13
 
-- Re-enable linting check for nextflow schema ([#354](https://github.com/nf-core/scrnaseq/pull/354))
+- Fix that tests have not been executed with nf-test v0.9 ([#359](https://github.com/nf-core/scrnaseq/pull/359))
 - Add support for 10XV4 chemistry ([#348](https://github.com/nf-core/scrnaseq/pull/348))
 - Fix issues with predefined STAR index ([#350](https://github.com/nf-core/scrnaseq/pull/350))
 - Update modules ([#351](https://github.com/nf-core/scrnaseq/pull/351))

nextflow.config

@@ -116,6 +116,11 @@ params {
     validationShowHiddenParams       = false
     validate_params                  = true
 
+    // TODO temporary workaround a warning
+    // not used anywhere and should not be necessary anymore after a nf-validation plugin update
+    // TODO when removing this, also remove the ignored lint check from .nf-core.yml
+    monochromeLogs = null
+
 }
 
 // Load base.config by default for all pipelines
@@ -249,7 +254,7 @@ singularity.registry = 'quay.io'
 
 // Nextflow plugins
 plugins {
-    id '[email protected].3' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+    id '[email protected].4' // Validation of pipeline parameters and creation of an input channel from a sample sheet
 }
 
 // Load igenomes.config if required