diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index a83427a4f179e30707d86342408a9a8e48c0ff44..848918b05640b2153343a07a4c3c4f1a5e4d70e7 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -8,6 +8,7 @@ before_script:
 
 stages:
   - unit
+  - integration
 
 getBag:
   stage: unit
@@ -36,4 +37,14 @@ trimData_pe:
   script:
   - if [ `nproc` -gt 8 ]; then ncore=8; else ncore=`nproc`; fi
   - singularity run 'docker://bicf/trimgalore:1.1' trim_galore --gzip -q 25 --illumina --length 35 --paired --basename Q-Y5JA -j ${ncore} ./test_data/fastq/Q-Y5JA.R1.fastq.gz ./test_data/fastq/Q-Y5JA.R2.fastq.gz
-  - pytest -m trimData_pe
\ No newline at end of file
+  - pytest -m trimData_pe
+
+integration_se:
+  stage: integration
+  script:
+  - nextflow run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID 16-1ZX4
+
+integration_pe:
+  stage: integration
+  script:
+  - nextflow run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5JA
\ No newline at end of file