kallisto index araport

.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

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

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_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

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