Merge branch 'master' of gitlab.pasteur.fr:hub/tars-cwl-runner

tars-cwl-runner.sh

@@ -5,13 +5,15 @@ singularity_imgs_path=/pasteur/projets/policy01/BioIT/Toil/.singularity_imgs/
 
 # Go into the right environment
 module load Python/3.7.2
+module load singularity/3.2.0
+module load node
 source ${toil_venv}/bin/activate
 
 export SINGULARITY_PULLFOLDER=${singularity_imgs_path}
 
 # Prefetch every docker images and built them for singularity
-docker_extract.py ${singularity_imgs_path} $1
+docker_extract.py -s ${singularity_imgs_path} $1
 
 # Run toil
 # export TOIL_SLURM_ARGS=""  # Need to be set by parameters later
-toil-cwl-runner "$@"
+toil-cwl-runner --singularity "$@"