diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index bd9fea32d00a7ce8367ae1084f63505aaafa7b0f..410aafb582422b102205f26a390c28bd77bc667b 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -205,8 +205,8 @@ countData:
   script:
   - ln -s /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/geneID.tsv
   - ln -s /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/Entrez.tsv
-  - singularity run 'docker://gudmaprbk/subread2.0.1:1.0.0' 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://gudmaprbk/subread2.0.1:1.0.0' Rscript ./workflow/scripts/calculateTPM.R --count ./test_data/counts/small/Q-Y5F6_1M.se.countData
+  - singularity run 'docker://gudmaprbk/subread2.0.1:1.0.0' 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://gudmaprbk/subread2.0.1:1.0.0' Rscript ./workflow/scripts/calculateTPM.R --count ./test_data/counts/small/Q-Y5F6_1M.se_countData
   - singularity run 'docker://gudmaprbk/subread2.0.1:1.0.0' Rscript ./workflow/scripts/convertGeneSymbols.R --repRID Q-Y5F6_1M.se
   - assignedReads=$(grep -m 1 'Assigned' *.summary | grep -oe '\([0-9.]*\)')
   - singularity run 'docker://gudmaprbk/subread2.0.1:1.0.0' featureCounts -v &> version_featurecounts.txt
diff --git a/workflow/tests/test_makeFeatureCounts.py b/workflow/tests/test_makeFeatureCounts.py
index f6373b99109e1d618dcb65559d24977140a125a4..e14793511b226a6c82d502ce2f84867c087bc41a 100644
--- a/workflow/tests/test_makeFeatureCounts.py
+++ b/workflow/tests/test_makeFeatureCounts.py
@@ -12,7 +12,7 @@ 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.countData'))
+        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(