Add ci nftests

.github/workflows/ci.yml

@@ -10,6 +10,8 @@ on:
 
 env:
   NXF_ANSI_LOG: false
+  CAPSULE_LOG: none
+  NFTEST_VER: "0.8.4"
 
 concurrency:
   group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
@@ -46,6 +48,22 @@ jobs:
       - name: Disk space cleanup
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - name: Run pipeline with test data
+      - name: Install nf-test
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.profile }},docker --outdir ./results
+          wget -qO- https://code.askimed.com/install/nf-test | bash -s $NFTEST_VER
+          sudo mv nf-test /usr/local/bin/
+
+      - name: Run nf-test
+        run: nf-test test tests/${{ 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 .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

.gitignore

@@ -7,3 +7,4 @@ testing/
 testing*
 *.pyc
 execution_trace*
+.nf-test*

tests/lib/UTILS.groovy

@@ -0,0 +1,11 @@
+// Function to remove Nextflow version from software_versions.yml
+
+class UTILS {
+    public static String removeNextflowVersion(outputDir) {
+        def softwareVersions = path("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml").yaml
+        if (softwareVersions.containsKey("Workflow")) {
+            softwareVersions.Workflow.remove("Nextflow")
+        }
+        return softwareVersions
+    }
+}

tests/test.nf.test

@@ -0,0 +1,27 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf - test"
+    script "main.nf"
+    profile "test"
+    tag "test"
+    tag "pipeline"
+
+    test("test") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") },
+                { assert workflow.trace.succeeded().size() == 196 }
+            )
+        }
+
+    }
+
+}

tests/test_index.nf.test

@@ -0,0 +1,27 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf - test_index"
+    script "main.nf"
+    profile "test_index"
+    tag "test_index"
+    tag "pipeline"
+
+    test("test_index") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") },
+                { assert workflow.trace.succeeded().size() == 161 }
+            )
+        }
+
+    }
+
+}

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 }
+            )
+        }
+
+    }
+
+}

tests/test_no_genome.nf.test

@@ -0,0 +1,27 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf - test_no_genome"
+    script "main.nf"
+    profile "test_no_genome"
+    tag "test_no_genome"
+    tag "pipeline"
+
+    test("test_no_genome") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") },
+                { assert workflow.trace.succeeded().size() == 147 }
+            )
+        }
+
+    }
+
+}

tests/test_technical_repeats.nf.test

@@ -0,0 +1,27 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf - test_technical_repeats"
+    script "main.nf"
+    profile "test_technical_repeats"
+    tag "test_technical_repeats"
+    tag "pipeline"
+
+    test("test_technical_repeats") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") },
+                { assert workflow.trace.succeeded().size() == 75 }
+            )
+        }
+
+    }
+
+}

tests/test_umi.nf.test

@@ -0,0 +1,27 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf - test_umi"
+    script "main.nf"
+    profile "test_umi"
+    tag "test_umi"
+    tag "pipeline"
+
+    test("test_umi") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") },
+                { assert workflow.trace.succeeded().size() == 64 }
+            )
+        }
+
+    }
+
+}