diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index d0d3b397bce47d83a4122ebc6d9f45392690b594..a2477d44d28efd3743bb5149c54c40c8eda0f1c0 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -106,7 +106,8 @@ countData:
   stage: unit
   script:
   - singularity run 'docker://bicf/subread2:2.0.0' featureCounts -T 20 -a /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/genome.gtf -G /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/genome.fna -g 'gene_name' --extraAttributes 'gene_id' -o Q-Y5F6_1M.se.countData -s 1 -R SAM --primary --ignoreDup ./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam 
-  - singularity run 'docker://bicf/subread2:2.0.0' Rscript ./workflow/scripts/calculateTPM.R --count ./test_data/counts/small/Q-Y5F6_1M.se.featureCounts
+  - singularity run 'docker://bicf/subread2:2.0.0' Rscript ./workflow/scripts/calculateTPM.R --count ./test_data/counts/small/Q-Y5F6_1M.se.countData
+  - singularity run 'docker://bicf/subread2:2.0.0' Rscript ./workflow/scripts/convertGeneSymbols.R --repRID Q-Y5F6_1M.se
   - assignedReads=$(grep -m 1 'Assigned' *.summary | grep -oe '\([0-9.]*\)')
   - pytest -m makeFeatureCounts
 
diff --git a/workflow/tests/test_makeFeatureCounts.py b/workflow/tests/test_makeFeatureCounts.py
index d741a2f4ac0f33fe15af8f13300c95002a00a887..d33527a9c7bffcaa9919639b72842cc8cf63b14f 100644
--- a/workflow/tests/test_makeFeatureCounts.py
+++ b/workflow/tests/test_makeFeatureCounts.py
@@ -11,5 +11,6 @@ data_output_path = os.path.dirname(os.path.abspath(__file__)) + \
 
 @pytest.mark.makeFeatureCounts
 def test_makeFeatureCounts():
-	assert os.path.exists(os.path.join(data_output_path, 'Q-Y5F6_1M.se.featureCounts'))
+	assert os.path.exists(os.path.join(data_output_path, 'Q-Y5F6_1M.se.countData'))
 	assert os.path.exists(os.path.join(data_output_path, 'Q-Y5F6_1M.se.countTable.csv'))
+	assert os.path.exists(os.path.join(data_output_path, 'Q-Y5F6_1M.se.tpmTable.csv'))