diff --git a/runs/kallisto_index/run.cwl b/runs/kallisto_index/run.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..6cbbb9cb2c9f62d41e333985bac086c08e91b9fa
--- /dev/null
+++ b/runs/kallisto_index/run.cwl
@@ -0,0 +1,36 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.2
+class: CommandLineTool
+
+hints:
+  DockerRequirement:
+    dockerPull: quay.io/biocontainers/kallisto:0.43.0--hdf51.8.17_2
+
+inputs:
+- id: sh_script
+  type: File
+  inputBinding:
+    position: 0
+- id: in_genome_ref
+  type: File
+  inputBinding:
+    position: 2
+- id: out_folder
+  type: string
+  inputBinding:
+    position: 3
+
+outputs:
+- id: outdir
+  type:
+    type: array
+    items: Directory
+  outputBinding:
+    glob: $(runtime.outdir)/$(inputs.out_folder)
+- id: example_out:
+  type: stdout
+stdout: output.txt
+
+baseCommand:
+- bash
diff --git a/runs/kallisto_index/run.yml b/runs/kallisto_index/run.yml
new file mode 100644
index 0000000000000000000000000000000000000000..57e15e409652ed9e212b66d13b72a9930647253e
--- /dev/null
+++ b/runs/kallisto_index/run.yml
@@ -0,0 +1,8 @@
+cores: 1
+sh_script:
+  class: File
+  path: ../../workflows/kallisto_index/kallisto_index.sh
+in_genome_ref:
+  class: File
+  path: ../../studies/ ##TODO
+out_folder: ./out
diff --git a/workflows/kallisto_index/kallisto_index.sh b/workflows/kallisto_index/kallisto_index.sh
new file mode 100644
index 0000000000000000000000000000000000000000..c346206eca3c0d7ec2294deb2387573e8d7926f8
--- /dev/null
+++ b/workflows/kallisto_index/kallisto_index.sh
@@ -0,0 +1,29 @@
+#!/usr/bin/env bash
+
+### Build kallisto index
+
+################################################
+#### Read arguments from CLI
+################################################
+
+in_genome_ref=$1
+out_folder=$2
+
+################################################
+#### Print version and citation to test kallisto 
+################################################
+
+kallisto version
+kallisto cite
+
+################################################
+#### If it does not exist, create out dir
+################################################
+
+mkdir -p $out_folder
+
+################################################
+#### Build kallisto index
+################################################
+
+kallisto index -i $out_folder/kallisto_index $in_genome_ref