diff --git a/workflows/kallisto/kallisto-help.cwl b/workflows/kallisto/kallisto-help.cwl
index c0dc2d24903c5900802525a7faff3f4b1a0f4d1d..dd42fae68ad46f33eb8800b65610889a3e9b1d40 100644
--- a/workflows/kallisto/kallisto-help.cwl
+++ b/workflows/kallisto/kallisto-help.cwl
@@ -4,15 +4,15 @@ class: CommandLineTool
 
 hints:
   DockerRequirement:
-    dockerPull: quay.io/biocontainers/kallisto:0.46.2--h4f7b962_1
+    dockerPull: quay.io/biocontainers/kallisto:0.51.0--h6de1650_0
   SoftwareRequirement:
     packages:
       kallisto:
-        version: [ "0.46.0" ]
+        version: [ "0.51.0" ]
         specs: [ https://identifiers.org/biotools/kallisto ]
 
 inputs: []
 
-baseCommand: [kallisto, index]
+baseCommand: [kallisto]
 
 outputs: []
\ No newline at end of file
diff --git a/workflows/kallisto/kallisto-index.cwl b/workflows/kallisto/kallisto-index.cwl
index 8813559db52913ca5a937c81c1d1e4438deaeb19..d37d620f19e19a7cfc7201a96cf6fdfdc8e0a2aa 100644
--- a/workflows/kallisto/kallisto-index.cwl
+++ b/workflows/kallisto/kallisto-index.cwl
@@ -1,14 +1,14 @@
 #!/usr/bin/env cwl-runner
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: CommandLineTool
 
 hints:
   DockerRequirement:
-    dockerPull: quay.io/biocontainers/kallisto:0.46.2--h4f7b962_1
+    dockerPull: quay.io/biocontainers/kallisto:0.51.0--h6de1650_0
   SoftwareRequirement:
     packages:
       kallisto:
-        version: [ "0.46.0" ]
+        version: [ "0.51.0" ]
         specs: [ https://identifiers.org/biotools/kallisto ]
 
 requirements:        
diff --git a/workflows/kallisto/kallisto-quant.cwl b/workflows/kallisto/kallisto-quant.cwl
index 9d6df5f0d6dd8502cecb916830c25685d3e791db..b3762212f8046a61254b9f67a8b1da15a34deeb7 100755
--- a/workflows/kallisto/kallisto-quant.cwl
+++ b/workflows/kallisto/kallisto-quant.cwl
@@ -1,14 +1,14 @@
 #!/usr/bin/env cwl-runner
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: CommandLineTool
 
 hints:
   DockerRequirement:
-    dockerPull: quay.io/biocontainers/kallisto:0.46.2--h4f7b962_1
+    dockerPull: quay.io/biocontainers/kallisto:0.51.0--h6de1650_0
   SoftwareRequirement:
     packages:
       kallisto:
-        version: [ "0.46.0" ]
+        version: [ "0.51.0" ]
         specs: [ https://identifiers.org/biotools/kallisto ]
 
 inputs: