diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 5152934a70a1e45f3d56915d4de805222334d14d..27cf3be2a30fb3bfdd1c49b3bbf07311818dba4a 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -58,8 +58,8 @@ alignReads:
 dedupReads:
   stage: unit
   script:
-  - singularity run 'docker://bicf/picard2.21.7:2.0.0' java -jar /picard/build/libs/picard.jar MarkDuplicates I=Q-Y5JA.sorted.bam O=Q-Y5JA.deduped.bam M=Q-Y5JA.deduped.Metrics.txt REMOVE_DUPLICATES=true
-  - singularity run 'docker://bicf/picard2.21.7:2.0.0' java -jar /picard/build/libs/picard.jar MarkDuplicates I=16-1ZX4.sorted.bam O=16-1ZX4.deduped.bam M=16-1ZX4.deduped.Metrics.txt REMOVE_DUPLICATES=true
+  - singularity exec 'docker://bicf/picard2.21.7:2.0.0' java -jar /picard/build/libs/picard.jar MarkDuplicates I=./test_data/bam/small/Q-Y5JA.sorted.bam O=./test_data/bam/small/Q-Y5JA.deduped.bam M=Q-Y5JA.deduped.Metrics.txt REMOVE_DUPLICATES=true
+  - singularity exec 'docker://bicf/picard2.21.7:2.0.0' java -jar /picard/build/libs/picard.jar MarkDuplicates I=./test_data/bam/small/16-1ZX4.sorted.bam O=./test_data/bam/small/16-1ZX4.deduped.bam M=16-1ZX4.deduped.Metrics.txt REMOVE_DUPLICATES=true
   - pytest -m dedupData
 
 integration_se: