Add runtime.exitCode to outputEval

Author: Peter Amstutz

cwltool/command_line_tool.py

@@ -592,12 +592,14 @@ def collect_output_ports(self,
                              ports,                  # type: Set[Dict[Text, Any]]
                              builder,                # type: Builder
                              outdir,                 # type: Text
+                             rcode,                  # type: int
                              compute_checksum=True,  # type: bool
                              jobname="",             # type: Text
                              readers=None            # type: Dict[Text, Any]
                             ):  # type: (...) -> OutputPorts
         ret = {}  # type: OutputPorts
         debug = _logger.isEnabledFor(logging.DEBUG)
+        builder.resources["exitCode"] = rcode
         try:
             fs_access = builder.make_fs_access(outdir)
             custom_output = fs_access.join(outdir, "cwl.output.json")

cwltool/job.py

@@ -328,7 +328,7 @@ def _execute(self,
                     self.generatemapper, self.outdir, self.builder.outdir,
                     inplace_update=self.inplace_update)
 
-            outputs = self.collect_outputs(self.outdir)
+            outputs = self.collect_outputs(self.outdir, rcode)
             outputs = bytes2str_in_dicts(outputs)  # type: ignore
         except OSError as e:
             if e.errno == 2: