diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 5a4263a167399c6d0aad20b83a7a232509af768b..10b06f97a6a83b23bdb1ac01e2ce46e975def353 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 -o .
   - pytest -m fastqc
 
 integration_se:
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 3cb62a5e64a72e27221dc89d87b828e02ae9405d..0fd3ee0d872768d1d7d80c0be6bcc0cbafd105e0 100755
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -354,6 +354,6 @@ process fastqc {
     ulimit -a >>${repRID}.fastqc.err
 
     # run fastqc
-    fastqc *.fastq.gz >>${repRID}.fastqc.err
+    fastqc *.fastq.gz -o . >>${repRID}.fastqc.err
     """
 }
\ No newline at end of file