diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 3643b929a0b3e95a465e9193d56e10ae3bec7f1f..be3baf25b29c9394058774e08757ca67fd97e675 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -56,11 +56,11 @@ alignData:
   - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' hisat2 -p `nproc` --add-chrname --un-gz Q-Y5JA_1M.se.unal.gz -S Q-Y5JA_1M.se.sam -x /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/hisat2/genome --rna-strandness F -U ./test_data/fastq/small/Q-Y5JA_1M_trimmed.fq.gz
   - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools view -1 -@ `nproc` -F 4 -F 8 -F 256 -o Q-Y5JA_1M.se.bam Q-Y5JA_1M.se.sam
   - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools sort -@ `nproc` -O BAM -o Q-Y5JA_1M.se.sorted.bam Q-Y5JA_1M.se.bam
-  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools index -@ `nproc` -b Q-Y5JA_1M.se.sorted.bam Q-Y5JA_1M.se.sorted.bai
+  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools index -@ `nproc` -b Q-Y5JA_1M.se.sorted.bam Q-Y5JA_1M.se.sorted.bam.bai
   - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' hisat2 -p `nproc` --add-chrname --un-gz Q-Y5JA_1M.pe.unal.gz -S Q-Y5JA_1M.pe.sam -x /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/hisat2/genome --rna-strandness FR --no-mixed --no-discordant -1 ./test_data/fastq/small/Q-Y5JA_1M_R1_val_1.fq.gz -2 ./test_data/fastq/small/Q-Y5JA_1M_R2_val_2.fq.gz
   - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools view -1 -@ `nproc` -F 4 -F 8 -F 256 -o Q-Y5JA_1M.pe.bam Q-Y5JA_1M.pe.sam
   - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools sort -@ `nproc` -O BAM -o Q-Y5JA_1M.pe.sorted.bam Q-Y5JA_1M.pe.bam
-  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools index -@ `nproc` -b Q-Y5JA_1M.pe.sorted.bam Q-Y5JA_1M.pe.sorted.bai
+  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools index -@ `nproc` -b Q-Y5JA_1M.pe.sorted.bam Q-Y5JA_1M.pe.sorted.bam.bai
   - pytest -m alignData
 
 dedupData:
@@ -68,7 +68,7 @@ dedupData:
   script:
   - 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.bai
+  - 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
   - pytest -m dedupData
   
 makeBigWig: