main.patch

--- main.py	2018-03-02 18:05:16.683793036 +0000
+++ main_new.py	2018-03-03 06:31:39.069337026 +0000
@@ -251,10 +251,21 @@
         raise WorkflowException("Must provide 'basedir' in kwargs")
 
     output_dirs = set()
+
+    #workflows run in the CGP will use the /datastore directory
+    #on the host to store all results. This has to be a fixed directory
+    #so that Docker containers created by other Docker containers
+    #can know its location ahead of time so they can access output 
+    #of other containers and can write results to the same directory
+    #Dockstore tool runner assumes all results are in /datastore
+    kwargs["outdir"] = '/datastore'
+    #Final results from the workflow in the CGP is stored in /datastore also
     finaloutdir = os.path.abspath(kwargs.get("outdir")) if kwargs.get("outdir") else None
-    kwargs["outdir"] = tempfile.mkdtemp(prefix=kwargs["tmp_outdir_prefix"]) if kwargs.get(
-        "tmp_outdir_prefix") else tempfile.mkdtemp()
+    #kwargs["outdir"] = tempfile.mkdtemp(prefix=kwargs["tmp_outdir_prefix"]) if kwargs.get(
+    #    "tmp_outdir_prefix") else tempfile.mkdtemp()
+
     output_dirs.add(kwargs["outdir"])
+
     kwargs["mutation_manager"] = MutationManager()
 
     jobReqs = None