diff --git a/.gitattributes b/.gitattributes
index a7b52de016f6eaa187fbab4c7db24dc59aa1e12d..5be99d5a806a4393e8ae9fa1e38a43ecce5f13b5 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -3,3 +3,4 @@ _publication/Image[[:space:]]1.pdf filter=lfs diff=lfs merge=lfs -text
 _publication/fpls-09-01709.pdf filter=lfs diff=lfs merge=lfs -text
 _publication/Data[[:space:]]Sheet[[:space:]]1.xlsx filter=lfs diff=lfs merge=lfs -text
 studies/arabidopsis-reference/resources/Araport11_genes.201606.cdna.fasta filter=lfs diff=lfs merge=lfs -text
+runs/kallisto_index/out/kallisto_index filter=lfs diff=lfs merge=lfs -text
diff --git a/runs/kallisto_index/out/kallisto_index b/runs/kallisto_index/out/kallisto_index
new file mode 100644
index 0000000000000000000000000000000000000000..91b51b9a0c8c7043b347935c5c1ae4dc74d0272e
--- /dev/null
+++ b/runs/kallisto_index/out/kallisto_index
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:8f1e4d00ef90de6f0b3fc3761e0996eb9e78b3e43eca1f0cb43fee5057f59bb7
+size 973267848
diff --git a/runs/kallisto_index/run.cwl b/runs/kallisto_index/run.cwl
index 6cbbb9cb2c9f62d41e333985bac086c08e91b9fa..06490aab04e8ebf21fe039e119d0e48f5a455b85 100644
--- a/runs/kallisto_index/run.cwl
+++ b/runs/kallisto_index/run.cwl
@@ -28,9 +28,6 @@ outputs:
     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.log b/runs/kallisto_index/run.log
new file mode 100644
index 0000000000000000000000000000000000000000..68630db036b1d2f52df207aa0f89bbd400eaf3e8
--- /dev/null
+++ b/runs/kallisto_index/run.log
@@ -0,0 +1,63 @@
+INFO /Users/dominikbrilhaus/opt/anaconda3/bin/cwltool 3.1.20240112164112
+INFO Resolved 'run.cwl' to 'file:///Users/dominikbrilhaus/gitlab_dataplant/hhu-plant-biochemistry/2018_SamuilovBrilhaus_BOU_DB/runs/kallisto_index/run.cwl'
+INFO [job run.cwl] /private/tmp/docker_tmp7lobn46w$ docker \
+    run \
+    -i \
+    --mount=type=bind,source=/private/tmp/docker_tmp7lobn46w,target=/OoJBhI \
+    --mount=type=bind,source=/private/tmp/docker_tmp18wvdt5m,target=/tmp \
+    --mount=type=bind,source=/Users/dominikbrilhaus/gitlab_dataplant/hhu-plant-biochemistry/2018_SamuilovBrilhaus_BOU_DB/workflows/kallisto_index/kallisto_index.sh,target=/var/lib/cwl/stg35dff622-c131-4e27-9e17-aff52d5d1d4a/kallisto_index.sh,readonly \
+    --mount=type=bind,source=/Users/dominikbrilhaus/gitlab_dataplant/hhu-plant-biochemistry/2018_SamuilovBrilhaus_BOU_DB/studies/arabidopsis-reference/resources/Araport11_genes.201606.cdna.fasta,target=/var/lib/cwl/stg1613bcd4-6884-48ed-9ab4-94385e70a5e6/Araport11_genes.201606.cdna.fasta,readonly \
+    --workdir=/OoJBhI \
+    --read-only=true \
+    --net=none \
+    --user=502:20 \
+    --rm \
+    --cidfile=/private/tmp/docker_tmp1e1fablo/20240125124956-101533.cid \
+    --env=TMPDIR=/tmp \
+    --env=HOME=/OoJBhI \
+    quay.io/biocontainers/kallisto:0.43.0--hdf51.8.17_2 \
+    bash \
+    /var/lib/cwl/stg35dff622-c131-4e27-9e17-aff52d5d1d4a/kallisto_index.sh \
+    /var/lib/cwl/stg1613bcd4-6884-48ed-9ab4-94385e70a5e6/Araport11_genes.201606.cdna.fasta \
+    ./out
+kallisto, version 0.43.0
+When using this program in your research, please cite
+
+  Bray, N. L., Pimentel, H., Melsted, P. & Pachter, L.
+  Near-optimal probabilistic RNA-seq quantification, 
+  Nature Biotechnology 34, 525-527(2016), doi:10.1038/nbt.3519
+
+
+[build] loading fasta file /var/lib/cwl/stg1613bcd4-6884-48ed-9ab4-94385e70a5e6/Araport11_genes.201606.cdna.fasta
+[build] k-mer length: 31
+[build] warning: clipped off poly-A tail (longer than 10)
+        from 14 target sequences
+[build] warning: replaced 11 non-ACGUT characters in the input sequence
+        with pseudorandom nucleotides
+[build] counting k-mers ... done.
+[build] building target de Bruijn graph ...  done 
+[build] creating equivalence classes ...  done
+[build] target de Bruijn graph has 173467 contigs and contains 45546882 k-mers 
+
+INFO [job run.cwl] Max memory used: 4869MiB
+INFO [job run.cwl] completed success
+{
+    "outdir": [
+        {
+            "location": "file:///Users/dominikbrilhaus/gitlab_dataplant/hhu-plant-biochemistry/2018_SamuilovBrilhaus_BOU_DB/runs/kallisto_index/out",
+            "basename": "out",
+            "class": "Directory",
+            "listing": [
+                {
+                    "class": "File",
+                    "location": "file:///Users/dominikbrilhaus/gitlab_dataplant/hhu-plant-biochemistry/2018_SamuilovBrilhaus_BOU_DB/runs/kallisto_index/out/kallisto_index",
+                    "basename": "kallisto_index",
+                    "size": 973267848,
+                    "checksum": "sha1$e7b7f9828f01a754b0373aaaa793089585580172",
+                    "path": "/Users/dominikbrilhaus/gitlab_dataplant/hhu-plant-biochemistry/2018_SamuilovBrilhaus_BOU_DB/runs/kallisto_index/out/kallisto_index"
+                }
+            ],
+            "path": "/Users/dominikbrilhaus/gitlab_dataplant/hhu-plant-biochemistry/2018_SamuilovBrilhaus_BOU_DB/runs/kallisto_index/out"
+        }
+    ]
+}INFO Final process status is success
diff --git a/runs/kallisto_index/run.yml b/runs/kallisto_index/run.yml
index 57e15e409652ed9e212b66d13b72a9930647253e..9f38d9993a7e0e0674554b18cc258aa3382dca3e 100644
--- a/runs/kallisto_index/run.yml
+++ b/runs/kallisto_index/run.yml
@@ -4,5 +4,5 @@ sh_script:
   path: ../../workflows/kallisto_index/kallisto_index.sh
 in_genome_ref:
   class: File
-  path: ../../studies/ ##TODO
+  path: ../../studies/arabidopsis-reference/resources/Araport11_genes.201606.cdna.fasta
 out_folder: ./out