diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 83783dd9e360e4dade57f721fa4bb83e7f0145e9..a2889e09f4f2973327bec6be6592f24199b3c6f8 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -69,6 +69,10 @@ dedupData:
   - singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' java -jar /picard/build/libs/picard.jar MarkDuplicates I=./test_data/bam/small/Q-Y5JA_1M.se.sorted.bam O=Q-Y5JA_1M.se.deduped.bam M=Q-Y5JA_1M.se.deduped.Metrics.txt REMOVE_DUPLICATES=true
   - singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' samtools sort -@ `nproc` -O BAM -o Q-Y5JA_1M.se.sorted.deduped.bam ./test_data/bam/small/Q-Y5JA_1M.se.deduped.bam
   - singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' samtools index -@ `nproc` -b ./test_data/bam/small/Q-Y5JA_1M.se.sorted.deduped.bam Q-Y5JA_1M.se.sorted.deduped.bam.bai
+  - singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' "
+      for i in {chr1,chr2,chr8}; do
+        echo \"samtools view -b Q-Y5JA_1M.se.sorted.deduped.bam ${i} > Q-Y5JA_1M.se.sorted.deduped.${i}.bam; samtools index -@ \`nproc\` -b Q-Y5JA_1M.se.sorted.deduped.${i}.bam Q-Y5JA_1M.se.sorted.deduped.${i}.bam.bai\" | parallel -j `nproc` -k
+        "
   - pytest -m dedupData
   
 makeBigWig: