change kallisto index to version used then

runs/kallisto_index/run.log

+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_tmpzx_cvyjo$ docker \
+    run \
+    -i \
+    --mount=type=bind,source=/private/tmp/docker_tmpzx_cvyjo,target=/eVdUYd \
+    --mount=type=bind,source=/private/tmp/docker_tmp4j2zkjbk,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/stg5f4efaa0-af92-4686-b8ef-77057f169cc5/kallisto_index.sh,readonly \
+    --mount=type=bind,source=/Users/dominikbrilhaus/gitlab_dataplant/hhu-plant-biochemistry/2018_SamuilovBrilhaus_BOU_DB/studies/arabidopsis-reference/resources/Arabidopsis_thaliana.TAIR10.28.cdna.all.fa,target=/var/lib/cwl/stg7d833517-acee-4e7a-b2b2-7ed5660b407c/Arabidopsis_thaliana.TAIR10.28.cdna.all.fa,readonly \
+    --workdir=/eVdUYd \
+    --read-only=true \
+    --net=none \
+    --user=502:20 \
+    --rm \
+    --cidfile=/private/tmp/docker_tmpjfamrngf/20240125141342-375856.cid \
+    --env=TMPDIR=/tmp \
+    --env=HOME=/eVdUYd \
+    quay.io/biocontainers/kallisto:0.43.0--hdf51.8.17_2 \
+    bash \
+    /var/lib/cwl/stg5f4efaa0-af92-4686-b8ef-77057f169cc5/kallisto_index.sh \
+    /var/lib/cwl/stg7d833517-acee-4e7a-b2b2-7ed5660b407c/Arabidopsis_thaliana.TAIR10.28.cdna.all.fa \
+    ./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/stg7d833517-acee-4e7a-b2b2-7ed5660b407c/Arabidopsis_thaliana.TAIR10.28.cdna.all.fa
+[build] k-mer length: 31
+[build] warning: clipped off poly-A tail (longer than 10)
+        from 24 target sequences
+[build] warning: replaced 698 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 290149 contigs and contains 47713570 k-mers 
+
+INFO [job run.cwl] Max memory used: 4931MiB
+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": 1029617006,
+                    "checksum": "sha1$4a16e2114b3e4c291d1d6d9c0e989532948a6a43",
+                    "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

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/arabidopsis-reference/resources/Araport11_genes.201606.cdna.fasta
+  path: ../../studies/arabidopsis-reference/resources/Arabidopsis_thaliana.TAIR10.28.cdna.all.fa
 out_folder: ./out