
# cwltool README

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

cd /Users/dominikbrilhaus/03_DataPLANT_gitlab/samplearc_rnaseq/runs/kallisto_sleuth

## Let it flow

```bash
### 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_sleuth.yml

### run with cwltool
cwltool ../../workflows/kallisto_sleuth.cwl kallisto_sleuth.yml

```
