Log which step workflow was on when an exception occurred. Tighten cwltool

check that input files exist and are regular files.

Author: Peter Amstutz

cwltool/job.py

@@ -47,8 +47,8 @@ def run(self, dry_run=False, pull_image=True, rm_container=True, rm_tmpdir=True,
         (docker_req, docker_is_req) = get_feature(self, "DockerRequirement")
 
         for f in self.pathmapper.files():
-            if not os.path.exists(self.pathmapper.mapper(f)[0]):
-                raise WorkflowException("Required input file %s not found" % self.pathmapper.mapper(f)[0])
+            if not os.path.isfile(self.pathmapper.mapper(f)[0]):
+                raise WorkflowException("Required input file %s not found or is not a regular file." % self.pathmapper.mapper(f)[0])
 
         img_id = None
         if docker_req and kwargs.get("use_container") is not False:

cwltool/workflow.py

@@ -472,6 +472,7 @@ def job(self, joborder, basedir, output_callback, **kwargs):
                                             **kwargs):
                 yield t
         except WorkflowException:
+            _logger.error("Exception on step '%s'", kwargs.get("name"))
             raise
         except Exception as e:
             _logger.exception("Unexpected exception")