Cromwell fails to return struct as output!

Cromwell cannot handle any output that is struct base. I enclose a workflow where it is very clear to see that even though both latest development versions (as well as latest releases) of Cromwell and Womtool validated and executed the workflow for some strange reason at runtime Cromwell consider that it is a Map and not a struct and crashes in the very end of execution

 QuantifiedRun quantified_run = {"run": srr, "folder": quant_folder, "quant": quant, "lib": quant_lib}

crashes_at_runtime.zip

[antonkulaga]

@aednichols I managed to get it working with:

    output {
        QuantifiedRun quantified_run = object {run: srr, folder: quant_folder, quant: quant, lib: quant_lib, metadata: info}
    }

However, I am very confused why it is working as object is supposed to be deprecated in development and because you have

Person a = {"name": "John","age": 30}

as a suggested syntax and you never mention that it does not work anymore. I think it is a documentation issue that you have

[AsierGonzalez]

@aednichols I managed to get it working with:

    output {
        QuantifiedRun quantified_run = object {run: srr, folder: quant_folder, quant: quant, lib: quant_lib, metadata: info}
    }

However, I am very confused why it is working as object is supposed to be deprecated in development and because you have

Person a = {"name": "John","age": 30}

as a suggested syntax and you never mention that it does not work anymore. I think it is a documentation issue that you have

This also worked for me. I had issues with a workflow that tried to use this struct:

struct SampleAndUnmappedBams {
  String base_file_name
  Array[File] flowcell_unmapped_bams
  String unmapped_bam_suffix
}

This wouldn’t work:

SampleAndUnmappedBams alignment_analysis_struct = {
    "base_file_name": sequencing_metadata.readgroup_name,
    "flowcell_unmapped_bams": [ Preprocessing.output_unmapped_bam ],
    "unmapped_bam_suffix": "unmapped.bam"
  }

But changing it to this did the trick:

SampleAndUnmappedBams alignment_analysis_struct = object {
    base_file_name: sequencing_metadata.readgroup_name,
    flowcell_unmapped_bams: [ Preprocessing.output_unmapped_bam ],
    unmapped_bam_suffix: "unmapped.bam"
  }

@Coppini, you can see that I am using an array of files in the struct and it worked, so at least that is solved now if it was really the issue.