README.md

cwltool README

First cd into the (runs) folder, with the .yml file

cd /Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq/runs/kallisto_quant

Let it flow

### store arc root (two levels up from here) as variable
arc_root=$(echo ${PWD%/*/*})

### replace arc root line in yml (specific to the machine from where this is run)
### not sure, if this works on linux... 
sed -i '' "s|^arc_root:.*|arc_root: $arc_root|g" kallisto_quant.yml

### run with cwltool
cwltool ../../workflows/kallisto_quant.cwl kallisto_index.yml