diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 41afb3fb547a74fb57f72912843889093d5e5c12..5a4263a167399c6d0aad20b83a7a232509af768b 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -70,7 +70,7 @@ dedupData:
 fastqc:
   stage: unit
   script:
-  - singularity run 'docker://bicf/fastqc:2.0.0' ./test_data/fastq/small/Q-Y5JA_1M.R1.fastq.gz
+  - singularity run 'docker://bicf/fastqc:2.0.0' ./test_data/fastq/small/Q-Y5JA_1M.R1.fastq.gz .
   - pytest -m fastqc
 
 integration_se: