From 4fa4157fe865029a01d69d45d6eca6dee7244af5 Mon Sep 17 00:00:00 2001
From: "Jeremiah H. Savage" <jeremiahsavage@gmail.com>
Date: Thu, 2 Jun 2016 18:34:57 -0500
Subject: [PATCH 1/2] when secondaryFiles is in an array, pass to each item

---
 cwltool/builder.py | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/cwltool/builder.py b/cwltool/builder.py
index 36d4663b4..e4da44a1a 100644
--- a/cwltool/builder.py
+++ b/cwltool/builder.py
@@ -107,8 +107,13 @@ 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":

From 583889991e6aa815bbaaf6fde4148f0790380b13 Mon Sep 17 00:00:00 2001
From: "Jeremiah H. Savage" <jeremiahsavage@gmail.com>
Date: Tue, 19 Jul 2016 15:36:20 -0500
Subject: [PATCH 2/2] stage files to outdir when using docker

---
 cwltool/job.py     | 2 +-
 cwltool/process.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

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: