Watch out for problematic values in manually supplied metrics for FDA report

[malachig]

I encountered this error:

Mar 10 10:45:13 malachi-immuno-mcdb024 java[14444]: 2023-03-10 10:45:13,121 cromwell-system-akka.dispatchers.engine-dispatcher-3541 INFO  - WorkflowManagerActor: Workflow 1c5196b6-0756-4d54-943d-59755d2198f0 failed (during ExecutingWorkflowState): java.lang.Exception: Task generateFdaMetricsForBamOrFastqs.generateFdaTables:NA:3 failed. The job was stopped before the command finished. PAPI error code 9. Execution failed: generic::failed_precondition: while running "/cromwell_root/script": unexpected exit status 2 was not ignored
Mar 10 10:45:13 malachi-immuno-mcdb024 java[14444]: [UserAction] Unexpected exit status 2 while running "/cromwell_root/script": /cromwell_root/script: line 42: syntax error near unexpected token `('
Mar 10 10:45:13 malachi-immuno-mcdb024 java[14444]: /cromwell_root/script: line 42: `      --spike_in_error_rate <=0.50% (R1), <=0.75% (R2) \'
Mar 10 10:45:13 malachi-immuno-mcdb024 java[14444]:         at cromwell.backend.google.pipelines.common.PipelinesApiAsyncBackendJobExecutionActor$.StandardException(PipelinesApiAsyncBackendJobExecutionActor.scala:91)

Which seems to be caused by this entry in my yaml: immuno.normal_dna_spike_in_error_rate: "<=0.50% (R1), <=0.75% (R2)"

Same idea would presumably apply to all the new inputs that allow a user to feed in values describing the data generation for the FDA QC report.

[malachig]

A second test, illustrated that any string with a space in it will also cause a failure.