add documentation about tars-cwl-runner script

README.md

@@ -2,6 +2,42 @@
 
 ## Usage
 
+## Description
+
+Here is a little description of what is going on in the `tars-cwl-runner.sh` script.
+
+### Load the right environment
+
+We need to load modules for:
+
+* Python3
+* Singularity
+* node (used for `javascript` expression within CWL
+
+Then we need to activate the `toil_venv`:
+
+```bash
+source ${toil_venv}/bin/activate
+```
+
+### Prefetch singularity images
+
+The script is run by the head of the cluster which is the only access point to internet.
+We do so to allow the automatic fetching of docker images (that are then built for singularity) and
+stored/cached into the `${singularity_imgs_path} folder.
+
+### Run toil
+
+When `cwltool` is used with the `--singularity` option, it can find the singularity images either in ([ref](https://github.com/common-workflow-language/cwltool/pull/1113)):
+
+* `$SINGULARITY_CACHEDIR`
+* `$SINGULARITY_PULLFOLDER`
+* current directory
+
+_Please note that your image follow a certain nomenclature. For a `repo/image` docker image, the
+expected name is `repo-image.img`. Every `:` and `/` are replaced by `-` and the `img` extension
+is expected at the end of the image name._
+
 ---------
 
 # Maintenance and Development