diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 24e6cbf1898ff6c5f1fd5827ebf03ee4eee1a8fd..28d51c4afe3c272631425ad253ae669574149bc2 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -11,7 +11,7 @@ qc_1:
     - pip install -r requirements.txt
     - pip install -r requirements_dev.txt
     - pip install -e .
-
+    
   script:
     - flake8 src/ setup.py
     - coverage run --source src/ -m pytest
@@ -25,7 +25,11 @@ test_1:
     - pip install -r requirements.txt
     - pip install -r requirements_dev.txt
     - pip install -e .
+    - apt update -y
+    - apt install wget -y
+    - wget -qO- https://get.nextflow.io | bash
+    - nextflow self-update
 
   script:
-    - python -m pytest
+    - nextflow main.nf
 
diff --git a/main.nf b/main.nf
new file mode 100755
index 0000000000000000000000000000000000000000..a740ba16c2123ca7f691eb61f5b4765bca965174
--- /dev/null
+++ b/main.nf
@@ -0,0 +1,34 @@
+/* 
+ * pipeline input parameters 
+ */
+params.annoFile = "$baseDir/inputs/ref_annotation.gt"
+params.copyNr = "$baseDir/inputs/transcript_tpms.txt"
+params.outdir = "results"
+
+log.info """\
+         R N A S E Q - N F   P I P E L I N E    
+         ===================================
+         annotation  : ${params.annoFile}
+         copy numbers: ${params.copyNr}
+         output dir       : ${params.outdir}
+         """
+         .stripIndent()
+
+ 
+/* 
+ * check that input files are there
+ */
+process mock {
+    
+    input:
+    path annoFile from params.annoFile
+    path copyNr from params.copyNr
+    
+    script:       
+    """
+    echo "Checked $annoFile and $copyNr"
+    """
+    
+}
+ 
+