diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 52488ed8..e78c8d3c 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -91,16 +91,16 @@ jobs:
           snakemake --cores 8 --use-conda
       - name: Generate md5sums
         run: |
-          md5sum data/processed/count_table.tsv > checksum.count_table
-          md5sum data/metadata/metadata.QC_applied.txt > checksum.metadata.QC_applied
-          md5sum analysis/QC/MultiQC_Report_data.zip > checksum.multiQC
-          md5sum analysis/QC/details/QC_per_sample.txt > checksum.QC_per_sample
-          md5sum analysis/DEG_lists/BaP/*.txt > checksums.BaP_DEGs
-          md5sum analysis/DEG_lists/CISP/*.txt > checksums.CISP_DEGs
-          # md5sum analysis/pathway_analysis/BaP/*WikiPathways* > checksums.BaP_pathways
-          # md5sum analysis/pathway_analysis/CISP/* > checksums.CISP_pathways
-          md5sum analysis/BMD_and_biomarker_files/*.txt > checksums.BMD_files
-          md5sum analysis/BMD_and_biomarker_files/*/*.txt >> checksums.BMD_files
+          md5sum output/processed/count_table.tsv > checksum.count_table
+          md5sum inputs/metadata/metadata.QC_applied.txt > checksum.metadata.QC_applied
+          md5sum output/QC/MultiQC_Report_data.zip > checksum.multiQC
+          md5sum output/QC/details/QC_per_sample.txt > checksum.QC_per_sample
+          md5sum output/analysis/analysis_default_????????_????/DEG_lists/BaP/*.txt > checksums.BaP_DEGs #wildcards for timestamped folder
+          md5sum output/analysis/analysis_default_????????_????/DEG_lists/CISP/*.txt > checksums.CISP_DEGs #wildcards for timestamped folder
+          # md5sum output/analysis/analysis_default_????????_????/pathway_analysis/BaP/*WikiPathways* > checksums.BaP_pathways
+          # md5sum output/analysis/analysis_default_????????_????/pathway_analysis/CISP/* > checksums.CISP_pathways
+          md5sum output/analysis/analysis_default_????????_????/BMD_and_biomarker_files/*.txt > checksums.BMD_files
+          md5sum output/analysis/analysis_default_????????_????/BMD_and_biomarker_files/*/*.txt >> checksums.BMD_files
       - name: Compare pre-processing and QC files to truth set
         run: |
           cmp truth_checksums/checksum.count_table checksum.count_table