Merge pull request #1265 from common-workflow-language/toil_aid

small tweaks to support toil

Author: mr-c

cwltool/docker.py

@@ -236,7 +236,7 @@ def append_volume(runtime, source, target, writable=False):
         runtime.append("--mount={}".format(mount_arg))
         # Unlike "--volume", "--mount" will fail if the volume doesn't already exist.
         if not os.path.exists(source):
-            os.mkdir(source)
+            os.makedirs(source)
 
     def add_file_or_directory_volume(
         self, runtime: List[str], volume: MapperEnt, host_outdir_tgt: Optional[str]

cwltool/pathmapper.py

@@ -326,8 +326,8 @@ def visit(self, obj, stagedir, basedir, copy=False, staged=False):
         elif obj["class"] == "File":
             path = obj["location"]
             ab = abspath(path, basedir)
-            if "contents" in obj and obj["location"].startswith("_:"):
-                self._pathmap[obj["location"]] = MapperEnt(
+            if "contents" in obj and path.startswith("_:"):
+                self._pathmap[path] = MapperEnt(
                     obj["contents"],
                     tgt,
                     "CreateWritableFile" if copy else "CreateFile",