Fix compatibility between toil and cwltool

.gitlab-ci.yml

@@ -173,7 +173,8 @@ build_doc:
   image: $INTEGRATION_IMAGE
   before_script:
     - apt-get update
-    - apt-get install -y make python3-sphinx
+    - apt-get install -y make
+    - pip install sphinx
   script:
     - cd docs
     - make html

Docker/Dockerfile-base

@@ -138,9 +138,7 @@ RUN wget https://bootstrap.pypa.io/get-pip.py && \
 
 # Install required python packages
 RUN python3 -m pip install --no-cache-dir --upgrade \
-    cwl-runner \
-    cwltool \
-    toil
+    toil[cwl]
 
 # Install current version of LINC. By adding this to the base image
 # we can speed up the build of the final image, because all of LINC's