diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
deleted file mode 100644
index 8ca00aa..0000000
--- a/.github/workflows/ci.yml
+++ /dev/null
@@ -1,40 +0,0 @@
-name: Pipeline CI
-
-on:
-  push:
-    branches:
-    - master
-    - dev
-  pull_request:
-    branches:
-    - master
-
-jobs:
-  build:
-
-    runs-on: ubuntu-latest
-
-    strategy:
-      fail-fast: false
-      matrix:
-        profile:
-            - gemflux
-            - starrsem
-            - starflux
-            - markdup
-            - rmdup
-            - ihec
-
-    steps:
-    - uses: actions/checkout@v3
-    - name: Set up Java
-      uses: actions/setup-java@v3
-      with:
-        distribution: zulu
-        java-version: 16
-        java-package: jre
-
-    - name: Run pipeline
-      run: . .circ && ci test
-      env:
-        CI_PROFILE: ${{ matrix.profile }}
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
new file mode 100644
index 0000000..0f06e8e
--- /dev/null
+++ b/.github/workflows/test.yml
@@ -0,0 +1,82 @@
+name: Test
+
+on:
+  push:
+    branches:
+      - master
+      - dev
+      - test-refactor
+  pull_request:
+    branches:
+      - master
+
+jobs:
+  pipeline-test:
+    name: Pipeline tests
+    runs-on: ubuntu-latest
+
+    strategy:
+      fail-fast: false
+      matrix:
+        profile:
+          - gemflux
+          - starrsem
+          - starflux
+          - markdup
+          - rmdup
+          - ihec
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Java
+        uses: actions/setup-java@v4
+        with:
+          distribution: zulu
+          java-version: 16
+          java-package: jre
+      - name: Setup Nextflow
+        uses: nf-core/setup-nextflow@v2
+      - name: Install nf-test
+        uses: nf-core/setup-nf-test@v1
+      - name: Run tests
+        run: nf-test test --tag pipeline --profile +${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
diff --git a/data/annotation.gtf.gz b/data/annotation.gtf.gz
new file mode 100644
index 0000000..c14a6a0
Binary files /dev/null and b/data/annotation.gtf.gz differ
diff --git a/data/genome.fa.gz b/data/genome.fa.gz
new file mode 100644
index 0000000..925b843
Binary files /dev/null and b/data/genome.fa.gz differ
diff --git a/tests/grape-pipeline-markdup.nf.test b/tests/grape-pipeline-markdup.nf.test
deleted file mode 100644
index 6d4c0f9..0000000
--- a/tests/grape-pipeline-markdup.nf.test
+++ /dev/null
@@ -1,29 +0,0 @@
-nextflow_pipeline {
-
-    name "Test Workflow grape-pipeline.nf"
-    script "grape-pipeline.nf"
-
-    profile "+markdup"
-    
-    test("Should run markdup pipeline") {
-
-        
-        when {
-            params {
-                // define parameters here. Example: 
-                // outdir = "tests/results"
-                steps = 'mapping'
-            }
-        }
-
-        then {
-            assert workflow.success
-            assert workflow.trace.failed().size() == 0
-            assert workflow.trace.succeeded().size() == 20
-            def lines = file("${launchDir}/pipeline.db").readLines()
-            assert lines.size() == 9
-        }
-
-    }
-
-}
diff --git a/tests/grape-pipeline-starrsem.nf.test b/tests/grape-pipeline-starrsem.nf.test
deleted file mode 100644
index 5c27ca1..0000000
--- a/tests/grape-pipeline-starrsem.nf.test
+++ /dev/null
@@ -1,29 +0,0 @@
-nextflow_pipeline {
-
-    name "Test Workflow grape-pipeline.nf"
-    script "grape-pipeline.nf"
-
-    profile "+starrsem"
-    
-    test("Should run starrsem pipeline") {
-
-        
-        when {
-            params {
-                // define parameters here. Example: 
-                // outdir = "tests/results"
-                steps = 'mapping'
-            }
-        }
-
-        then {
-            assert workflow.success
-            assert workflow.trace.failed().size() == 0
-            assert workflow.trace.succeeded().size() == 17
-            def lines = file("${launchDir}/pipeline.db").readLines()
-            assert lines.size() == 9
-        }
-
-    }
-
-}
diff --git a/tests/grape-pipeline.nf.test b/tests/grape-pipeline.nf.test
new file mode 100644
index 0000000..5099532
--- /dev/null
+++ b/tests/grape-pipeline.nf.test
@@ -0,0 +1,37 @@
+import com.askimed.nf.test.util.AnsiColors;
+import com.askimed.nf.test.util.AnsiText;
+
+nextflow_pipeline {
+
+    name "Test Workflow grape-pipeline.nf"
+    script "grape-pipeline.nf"
+
+    tag "pipeline"
+
+    test("Should run pipeline") {
+
+        setup {
+            def profile = parent.profiles.last().minus('+')
+            print "(${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
+        }
+
+    }
+
+}
diff --git a/tests/modules/fastaIndex/samtools/main.nf.test b/tests/modules/fastaIndex/samtools/main.nf.test
index 44ac97a..3d87f0b 100644
--- a/tests/modules/fastaIndex/samtools/main.nf.test
+++ b/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 {
diff --git a/tests/modules/mapping/star/main.index.nf.test b/tests/modules/mapping/star/main.index.nf.test
index f09a2f7..466c4f8 100644
--- a/tests/modules/mapping/star/main.index.nf.test
+++ b/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 {
diff --git a/tests/workflows/mapping.nf.test b/tests/workflows/mapping.nf.test
index 84e7a07..288638d 100644
--- a/tests/workflows/mapping.nf.test
+++ b/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 {
                 """