Minimal profiles for testing ci settings

.github/workflows/ci.yml

@@ -1,53 +1,34 @@
 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
-  NFT_VER: "0.8.4"
-  NFT_WORKDIR: "~"
-  NFT_DIFF: "pdiff"
-  NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2"
+  CAPSULE_LOG: none
+  NFTEST_VER: "0.8.4"
 
 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 != '[]'
+    name: Run pipeline with test data
+    # Only run on push if this is the nf-core dev branch (merged PRs)
+    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/smrnaseq') }}"
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
         NXF_VER:
+          - "23.04.0"
           - "latest-everything"
-          - "23.04"
-        nf_test_files: ["${{ fromJson(needs.nf-test-changes.outputs.nf_test_files) }}"]
         profile:
           - "test"
           - "test_no_genome"
@@ -64,53 +45,25 @@ jobs:
         with:
           version: "${{ matrix.NXF_VER }}"
 
-      - uses: actions/setup-python@v4
-        with:
-          python-version: "3.11"
-          architecture: "x64"
+      - name: Disk space cleanup
+        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - name: Install pdiff to see diff between nf-test snapshots
+      - name: Install nf-test
         run: |
-          python -m pip install --upgrade pip
-          pip install pdiff
-
-      - uses: nf-core/setup-nf-test@v1
+          wget -qO- https://code.askimed.com/install/nf-test | bash -s $NFTEST_VER
+          sudo mv nf-test /usr/local/bin/
 
       - name: Run nf-test
-        run: |
-          nf-test test --verbose ${{ matrix.nf_test_files }} --profile "+${{ matrix.profile }}" --junitxml=test.xml --tap=test.tap
-
-      - uses: pcolby/tap-summary@v1
-        with:
-          path: >-
-            test.tap
+        run: nf-test test tests/${{ matrix.profile }}.nf.test --profile +docker --junitxml=test.xml
 
       - 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
+          batcat --decorations=always --color=always .nf-test/tests/*/output/pipeline_info/software_versions.yml
 
       - 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) }}"

tests/test_mirgenedb.nf.test

@@ -0,0 +1,27 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf - test_mirgenedb"
+    script "main.nf"
+    profile "test_mirgenedb"
+    tag "test_mirgenedb"
+    tag "pipeline"
+
+    test("test_mirgenedb") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") },
+                { assert workflow.trace.succeeded().size() == 193 }
+            )
+        }
+
+    }
+
+}