Merge branch '10165-cwl-outputs' closes #10165

diff --combined sdk/cwl/arvados_cwl/runner.py
index a4132ca3f762675ff9dccc0129f3f8139b313f1b,c52c952abf0569358356b53903859b26c85d87e5..e5b4e006e8cce7cac780436fc06c6dcd79882730
--- 1/sdk/cwl/arvados_cwl/runner.py
--- 2/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@@ -21,7 -21,7 +21,7 @@@ from .pathmapper import ArvPathMappe
  
  logger = logging.getLogger('arvados.cwl-runner')
  
 -cwltool.draft2tool.ACCEPTLIST_RE = re.compile(r"^[a-zA-Z0-9._+-]+$")
 +cwltool.draft2tool.ACCEPTLIST_RE = re.compile(r".*")
  
  def trim_listing(obj):
      """Remove 'listing' field from Directory objects that are keep references.
@@@ -114,13 -114,15 +114,15 @@@ def upload_docker(arvrunner, tool)
  
  
  class Runner(object):
-     def __init__(self, runner, tool, job_order, enable_reuse):
+     def __init__(self, runner, tool, job_order, enable_reuse, output_name):
          self.arvrunner = runner
          self.tool = tool
          self.job_order = job_order
          self.running = False
          self.enable_reuse = enable_reuse
          self.uuid = None
+         self.final_output = None
+         self.output_name = output_name
  
      def update_pipeline_component(self, record):
          pass
@@@ -169,7 -171,11 +171,11 @@@
          outputs = None
          try:
              try:
-                 outc = arvados.collection.Collection(record["output"])
+                 self.final_output = record["output"]
+                 outc = arvados.collection.CollectionReader(self.final_output,
+                                                            api_client=self.arvrunner.api,
+                                                            keep_client=self.arvrunner.keep_client,
+                                                            num_retries=self.arvrunner.num_retries)
                  with outc.open("cwl.output.json") as f:
                      outputs = json.load(f)
                  def keepify(fileobj):