diff --git a/.gitattributes b/.gitattributes
index 9c9b3910e5de35f7b58c8bffdaea119b0999cc19..07a4a56143d25a23ce6ab0320d147c3096caa5f6 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -27,9 +27,9 @@
 /assays/Talinum_RNASeq_minimal/dataset/DB_161_reC3MD_GTCCGC_L001_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text
 /assays/Talinum_RNASeq_minimal/dataset/DB_163_reC3MD_GTGAAA_L001_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text
 /assays/Talinum_RNASeq_minimal/dataset/DB_165_re-C3MD_GTGAAA_L002_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text
-runs/kallisto_collect/kallisto_df.csv filter=lfs diff=lfs merge=lfs -text
+runs/sleuth/kallisto_df.csv filter=lfs diff=lfs merge=lfs -text
 runs/kallisto_sleuth/sleuth_dge.csv filter=lfs diff=lfs merge=lfs -text
 studies/TalinumGenomeDraft/resources/Talinum.gm.CDS.nt.fa filter=lfs diff=lfs merge=lfs -text
-runs/kallisto_collect/kallisto_sleuthObject.RData filter=lfs diff=lfs merge=lfs -text
-runs/kallisto_collect/out/kallisto_sleuthObject.RData filter=lfs diff=lfs merge=lfs -text
+runs/sleuth/kallisto_sleuthObject.RData filter=lfs diff=lfs merge=lfs -text
+runs/sleuth/out/kallisto_sleuthObject.RData filter=lfs diff=lfs merge=lfs -text
 runs/kallisto/kallisto_results/** filter=lfs diff=lfs merge=lfs -text
\ No newline at end of file
diff --git a/runs/shiny_prep/run.yml b/runs/shiny_prep/run.yml
index 7124f42d4bf3c475754e9f72ef0bddfd7c4d9dc7..8e7954b4766c5dabe9c6c4bac267ad186782abef 100644
--- a/runs/shiny_prep/run.yml
+++ b/runs/shiny_prep/run.yml
@@ -4,5 +4,5 @@ r_script:
   path: ../../workflows/shiny_prep/shiny_prep.R
 in_kallisto_df: 
   class: File
-  path: ../kallisto_collect/out/kallisto_df.csv
+  path: ../sleuth/out/kallisto_df.csv
 out_folder: out
\ No newline at end of file
diff --git a/runs/kallisto_collect/results/kallisto_df.csv b/runs/sleuth/results/kallisto_df.csv
similarity index 100%
rename from runs/kallisto_collect/results/kallisto_df.csv
rename to runs/sleuth/results/kallisto_df.csv
diff --git a/runs/kallisto_collect/results/kallisto_mappingStats.csv b/runs/sleuth/results/kallisto_mappingStats.csv
similarity index 100%
rename from runs/kallisto_collect/results/kallisto_mappingStats.csv
rename to runs/sleuth/results/kallisto_mappingStats.csv
diff --git a/runs/kallisto_collect/results/kallisto_sleuthObject.RData b/runs/sleuth/results/kallisto_sleuthObject.RData
similarity index 100%
rename from runs/kallisto_collect/results/kallisto_sleuthObject.RData
rename to runs/sleuth/results/kallisto_sleuthObject.RData
diff --git a/runs/kallisto_collect/results/kallisto_tpmMatrix.csv b/runs/sleuth/results/kallisto_tpmMatrix.csv
similarity index 100%
rename from runs/kallisto_collect/results/kallisto_tpmMatrix.csv
rename to runs/sleuth/results/kallisto_tpmMatrix.csv
diff --git a/runs/kallisto_collect/results/sleuth_dge.csv b/runs/sleuth/results/sleuth_dge.csv
similarity index 100%
rename from runs/kallisto_collect/results/sleuth_dge.csv
rename to runs/sleuth/results/sleuth_dge.csv
diff --git a/runs/kallisto_collect/run.cwl b/runs/sleuth/run.cwl
similarity index 91%
rename from runs/kallisto_collect/run.cwl
rename to runs/sleuth/run.cwl
index 302db8da4c71bc3fb0ecec0319617732bdc5871d..b21434225a867157c64962fcf079f36b19d302b5 100644
--- a/runs/kallisto_collect/run.cwl
+++ b/runs/sleuth/run.cwl
@@ -13,7 +13,7 @@ inputs:
 
 steps: 
   collectResults:
-    run: ../../workflows/kallisto_collect/workflow.cwl
+    run: ../../workflows/sleuth/workflow.cwl
     in:
       inKallistoResults: inKallistoResults
       inMetadataFile: inMetadataFile
diff --git a/runs/kallisto_collect/run.yml b/runs/sleuth/run.yml
similarity index 100%
rename from runs/kallisto_collect/run.yml
rename to runs/sleuth/run.yml
diff --git a/workflows/kallisto_collect/Dockerfile b/workflows/sleuth/Dockerfile
similarity index 100%
rename from workflows/kallisto_collect/Dockerfile
rename to workflows/sleuth/Dockerfile
diff --git a/workflows/kallisto_collect/kallisto_collect.R b/workflows/sleuth/sleuth.R
similarity index 100%
rename from workflows/kallisto_collect/kallisto_collect.R
rename to workflows/sleuth/sleuth.R
diff --git a/workflows/kallisto_collect/workflow.cwl b/workflows/sleuth/workflow.cwl
similarity index 89%
rename from workflows/kallisto_collect/workflow.cwl
rename to workflows/sleuth/workflow.cwl
index 1b182ead03cac467ae75550df77ac9677dca0054..8163e27b260d56b501b3e5f0ad8a95ffb4586649 100644
--- a/workflows/kallisto_collect/workflow.cwl
+++ b/workflows/sleuth/workflow.cwl
@@ -13,13 +13,13 @@ hints:
 requirements:
   - class: InitialWorkDirRequirement
     listing:
-      - entryname: kallisto_collect.R
+      - entryname: sleuth.R
         entry:
-          $include: kallisto_collect.R
+          $include: sleuth.R
   - class: NetworkAccess
     networkAccess: true
 
-baseCommand: [Rscript, kallisto_collect.R]
+baseCommand: [Rscript, sleuth.R]
 
 inputs:
   inKallistoResults: