Only count output file usage when using the file store (#4692)

src/toil/cwl/cwltoil.py

@@ -2265,13 +2265,20 @@ def __init__(
                 )
             preemptible = parsed_value
 
+        # We always need space for the temporary files for the job
+        total_disk = cast(int, req["tmpdirSize"]) * (2**20)
+        if not getattr(runtime_context, "bypass_file_store", False):
+            # If using the Toil file store, we also need space for the output
+            # files, which may need to be stored locally and copied off the
+            # node.
+            total_disk += cast(int, req["outdirSize"]) * (2**20)
+        # If not using the Toil file store, output files just go directly to
+        # their final homes their space doesn't need to be accounted per-job.
+
         super().__init__(
             cores=req["cores"],
             memory=int(req["ram"] * (2**20)),
-            disk=int(
-                (cast(int, req["tmpdirSize"]) * (2**20))
-                + (cast(int, req["outdirSize"]) * (2**20))
-            ),
+            disk=int(total_disk),
             accelerators=accelerators,
             preemptible=preemptible,
             tool_id=self.cwltool.tool["id"],