diff --git a/cwltool/builder.py b/cwltool/builder.py
index d66b98888..c36a096c6 100644
--- a/cwltool/builder.py
+++ b/cwltool/builder.py
@@ -96,8 +96,13 @@ def bind_input(self, schema, datum, lead_pos=[], tail_pos=[]):
                     if binding:
                         b2 = copy.deepcopy(binding)
                         b2["valueFrom"] = item
-                    bindings.extend(self.bind_input({"type": schema["items"], "inputBinding": b2},
-                                                    item, lead_pos=n, tail_pos=tail_pos))
+                    if "secondaryFiles" in schema:
+                        bindings.extend(self.bind_input({"type": schema["items"], "inputBinding": b2,
+                                                         "secondaryFiles" : schema["secondaryFiles"]},
+                                                        item, lead_pos=n, tail_pos=tail_pos))
+                    else:
+                        bindings.extend(self.bind_input({"type": schema["items"], "inputBinding": b2},
+                                                        item, lead_pos=n, tail_pos=tail_pos))
                 binding = None
 
             if schema["type"] == "File":
diff --git a/cwltool/job.py b/cwltool/job.py
index 1a0b51548..5017d86de 100644
--- a/cwltool/job.py
+++ b/cwltool/job.py
@@ -183,7 +183,7 @@ def linkoutdir(src, tgt):
                     # the container)
                     for _, item in self.pathmapper.items():
                         if src == item.resolved:
-                            os.symlink(item.target, tgt)
+                            os.symlink(src, tgt)
                             break
                 stageFiles(generatemapper, linkoutdir)
 
diff --git a/cwltool/process.py b/cwltool/process.py
index a2b63115c..36e05fe66 100644
--- a/cwltool/process.py
+++ b/cwltool/process.py
@@ -420,7 +420,7 @@ def _init_job(self, joborder, **kwargs):
             raise WorkflowException("Document has DockerRequirement under 'requirements' but use_container is false.  DockerRequirement must be under 'hints' or use_container must be true.")
 
         if dockerReq and kwargs.get("use_container"):
-            builder.outdir = kwargs.get("docker_outdir") or "/var/spool/cwl"
+            builder.outdir = kwargs.get("outdir") or "/var/spool/cwl"
             builder.tmpdir = kwargs.get("docker_tmpdir") or "/tmp"
             builder.stagedir = kwargs.get("docker_stagedir") or "/var/lib/cwl"
         else: