cwltool: upgrade to the latest version

closes reanahub/reana-workflow-engine-cwl#187

reana_client/cli/cwl_runner.py

@@ -22,7 +22,6 @@
 from cwltool.context import LoadingContext
 from cwltool.load_tool import fetch_document
 from cwltool.main import printdeps
-from cwltool.workflow import findfiles
 
 from reana_client.cli.utils import add_access_token_options
 from reana_client.config import default_user
@@ -32,6 +31,23 @@
 PY3 = sys.version_info > (3,)
 
 
+def findfiles(wo, fn=None):
+    """Return a list CWL workflow files."""
+    if fn is None:
+        fn = []
+    if isinstance(wo, dict):
+        if wo.get("class") == "File":
+            fn.append(wo)
+            findfiles(wo.get("secondaryFiles", None), fn)
+        else:
+            for w in wo.values():
+                findfiles(w, fn)
+    elif isinstance(wo, list):
+        for w in wo:
+            findfiles(w, fn)
+    return fn
+
+
 def get_file_dependencies_obj(cwl_obj, basedir):
     """Return a dictionary which contains the CWL workflow file dependencies.
 

setup.py

@@ -44,8 +44,7 @@
 install_requires = [
     'click>=7 ; python_version>="3"',
     'click==7.0 ; python_version=="2.7"',
-    "cwltool==1.0.20191022103248",
-    'cwl-utils==0.5 ; python_version>="3"',
+    "cwltool==3.1.20210628163208",
     "jsonpointer>=2.0",
     "PyYAML>=5.1",
     "reana-commons[yadage]>=0.8.0a17,<0.9.0",