Merge master into issues/5120-wdl-normalize-trouble

src/toil/test/cwl/cwlTest.py

@@ -476,7 +476,6 @@ def test_slurm_node_memory(self) -> None:
             "--outdir",
             self.outDir,
             os.path.join(self.rootDir, "src/toil/test/cwl/measure_default_memory.cwl"),
-            os.path.join(self.rootDir, "src/toil/test/cwl/empty.json"),
         ]
         try:
             log.debug("Start test workflow")
@@ -497,7 +496,7 @@ def test_slurm_node_memory(self) -> None:
         else:
             out = json.loads(output)
             log.debug("Workflow output: %s", out)
-            memory_string = open(out["memory"]["location"][len("file://") :]).read()
+            memory_string = out["memory"]
             log.debug("Observed memory: %s", memory_string)
             result = int(memory_string)
             # We should see more than the CWL default or the Toil default, assuming Slurm nodes of reasonable size (3 GiB).

src/toil/test/cwl/measure_default_memory.cwl

@@ -1,23 +1,12 @@
 cwlVersion: v1.2
-class: Workflow
-
+class: CommandLineTool
 inputs: []
-
-steps:
-  measure:
-    run:
-      class: CommandLineTool
-      inputs: []
-      baseCommand: ["bash", "-c", "ulimit -m"]
-      outputs:
-        memory: stdout
-    in: []
-    out:
-      # There's no good way to go back from a command output to a CWL value
-      # without bringing in a bunch of JS.
-      - id: memory
-
+baseCommand: ["bash", "-c", "ulimit -m"]
+stdout: memory.txt
 outputs:
-  - id: memory
-    type: File
-    outputSource: measure/memory
+  memory:
+    type: string
+    outputBinding:
+      glob: memory.txt
+      loadContents: True
+      outputEval: $(self[0].contents)