Fix: AWS Batch with CWL: did not localize cwl.inputs.json [BA-4586]

backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala

@@ -268,6 +268,12 @@ trait StandardAsyncExecutionActor
   def cwd: Path = commandDirectory
   def rcPath: Path = cwd./(jobPaths.returnCodeFilename)
 
+  /**
+    * Directory where workflow user commands will be executed.
+    * It's overridden in AwsBatchAsyncBackendJobExecutionActor in order to allow Cromwell find adHoc files.
+    * */
+  def adHocCwd: String = cwd.pathAsString
+
   // The standard input filename can be as ephemeral as the execution: the name needs to match the expectations of
   // the command, but the standard input file will never be accessed after the command completes. standard output and
   // error on the other hand will be accessed and the names of those files need to be known to be delocalized and read
@@ -383,7 +389,7 @@ trait StandardAsyncExecutionActor
         |tee $stdoutRedirection < "$$$out" &
         |tee $stderrRedirection < "$$$err" >&2 &
         |(
-        |cd $cwd
+        |cd $adHocCwd
         |ENVIRONMENT_VARIABLES
         |INSTANTIATED_COMMAND
         |) $stdinRedirection > "$$$out" 2> "$$$err"

centaur/src/main/resources/standardTestCases/ad_hoc_file_test.aws.test

@@ -0,0 +1,14 @@
+name: ad_hoc_file_test.aws
+testFormat: workflowsuccess
+backends: [ AWSBATCH ]
+
+files {
+  workflow: ad_hoc_file_test/workflow.cwl
+  imports: [
+    ad_hoc_file_test/cwl-test.cwl
+  ]
+}
+
+metadata {
+  status: Succeeded
+}

centaur/src/main/resources/standardTestCases/ad_hoc_file_test/cwl-test.cwl

@@ -0,0 +1,21 @@
+class: CommandLineTool
+cwlVersion: v1.0
+baseCommand: ["sh", "example.sh"]
+hints:
+  DockerRequirement:
+    dockerPull: ubuntu:latest
+inputs: []
+
+requirements:
+  InitialWorkDirRequirement:
+    listing:
+      - entryname: example.sh
+        entry: |-
+          PREFIX='Message is:'
+          MSG="\${PREFIX} Hello world!"
+          echo \${MSG}
+
+outputs:
+  example_out:
+    type: stdout
+stdout: output.txt

centaur/src/main/resources/standardTestCases/ad_hoc_file_test/workflow.cwl

@@ -0,0 +1,10 @@
+cwlVersion: v1.0
+class: Workflow
+inputs: []
+outputs: []
+
+steps:
+  test:
+    run: cwl-test.cwl
+    in: []
+    out: []

supportedBackends/aws/src/main/scala/cromwell/backend/impl/aws/AwsBatchAsyncBackendJobExecutionActor.scala

@@ -345,6 +345,8 @@ class AwsBatchAsyncBackendJobExecutionActor(override val standardParams: Standar
     disk.mountPoint
   }
 
+  override def adHocCwd = runtimeEnvironment.outputPath
+
   override def isTerminal(runStatus: RunStatus): Boolean = {
     runStatus match {
       case _: TerminalRunStatus => true