Update tests and GitHub action

.github/workflows/test.yml

@@ -0,0 +1,82 @@
+name: Test
+
+on:
+  push:
+    branches:
+      - master
+      - dev
+      - test-refactor
+  pull_request:
+    branches:
+      - master
+
+jobs:
+  pipeline-test:
+    name: Pipeline tests
+    runs-on: ubuntu-latest
+
+    strategy:
+      fail-fast: false
+      matrix:
+        profile:
+          - gemflux
+          - starrsem
+          - starflux
+          - markdup
+          - rmdup
+          - ihec
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Java
+        uses: actions/setup-java@v4
+        with:
+          distribution: zulu
+          java-version: 16
+          java-package: jre
+      - name: Setup Nextflow
+        uses: nf-core/setup-nextflow@v2
+      - name: Install nf-test
+        uses: nf-core/setup-nf-test@v1
+      - name: Run tests
+        run: nf-test test --tag pipeline --profile +${CI_PROFILE}
+        env:
+          CI_PROFILE: ${{ matrix.profile }}
+
+  workflow-test:
+    name: Workflow tests
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Java
+        uses: actions/setup-java@v3
+        with:
+          distribution: zulu
+          java-version: 16
+          java-package: jre
+      - name: Setup Nextflow
+        uses: nf-core/setup-nextflow@v2
+      - name: Install nf-test
+        uses: nf-core/setup-nf-test@v1
+      - name: Run tests
+        run: nf-test test --tag workflow
+
+  module-test:
+    name: Module tests
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Java
+        uses: actions/setup-java@v3
+        with:
+          distribution: zulu
+          java-version: 16
+          java-package: jre
+      - name: Setup Nextflow
+        uses: nf-core/setup-nextflow@v2
+      - name: Install nf-test
+        uses: nf-core/setup-nf-test@v1
+      - name: Run tests
+        run: nf-test test --tag module

tests/grape-pipeline.nf.test

@@ -0,0 +1,37 @@
+import com.askimed.nf.test.util.AnsiColors;
+import com.askimed.nf.test.util.AnsiText;
+
+nextflow_pipeline {
+
+    name "Test Workflow grape-pipeline.nf"
+    script "grape-pipeline.nf"
+
+    tag "pipeline"
+
+    test("Should run pipeline") {
+
+        setup {
+            def profile = parent.profiles.last().minus('+')
+            print "(${AnsiColors.yellow(profile)}) "
+        }
+
+        then {
+            def profile = parent.profiles.last().minus('+')
+            def expected = [
+                "starrsem": [ traceSize: 28, dbSize: 30 ],
+                "starflux": [ traceSize: 24, dbSize: 28 ],
+                 "markdup": [ traceSize: 31, dbSize: 30 ],
+                 "gemflux": [ traceSize: 24, dbSize: 22 ],
+                   "rmdup": [ traceSize: 31, dbSize: 30 ],
+                    "ihec": [ traceSize: 31, dbSize: 30 ],
+            ][profile]
+            assert workflow.success
+            assert workflow.trace.failed().size() == 0
+            assert workflow.trace.succeeded().size() == expected?.traceSize
+            def lines = file("${launchDir}/pipeline.db").readLines()
+            assert lines.size() == expected?.dbSize
+        }
+
+    }
+
+}

tests/modules/fastaIndex/samtools/main.nf.test

@@ -4,6 +4,8 @@ nextflow_process {
     script "modules/fastaIndex/samtools/main.nf"
     process "fastaIndex"
 
+    tag "module"
+
     test("Should produce the fasta index") {
 
         when {

tests/modules/mapping/star/main.index.nf.test

@@ -3,7 +3,9 @@ nextflow_process {
     name "Test Process index"
     script "modules/mapping/star/main.nf"
     process "index"
-
+
+    tag "module"
+
     test("Should index compressed references") {
 
         when {

tests/workflows/mapping.nf.test

@@ -4,6 +4,8 @@ nextflow_workflow {
     script "workflows/mapping.nf"
     workflow "mapping"
 
+    tag "workflow"
+
     test("Should run STAR mapping sorting with sambamba") {
 
         when {
@@ -13,7 +15,7 @@ nextflow_workflow {
                 sortBamTool = "sambamba"
                 sjOverHang = 100
                 maxMismatches = 4
-                maxMultimaps = 10    
+                maxMultimaps = 10
             }
             workflow {
                 """
@@ -49,7 +51,7 @@ nextflow_workflow {
                 sortBamTool = "samtools"
                 sjOverHang = 100
                 maxMismatches = 4
-                maxMultimaps = 10    
+                maxMultimaps = 10
             }
             workflow {
                 """