scatter over optional array

Post author
tariq nawaz

I have a case where I want to iterate over two arrays, one of which shall be optionally present or not. I created the test WDL below. In the case of create_inner_array = false it throws the error

Failed to evaluate input 'CreateArray.echo' (reason 1 of 1): Failed to lookup input value for required input echo

But in the case of create_inner_array = true it throws the error

assertion failed: base member type WomMaybeEmptyArrayType(WomOptionalType(WomAnyType)) and womtype WomMaybeEmptyArrayType(WomOptionalType(WomStringType)) are not compatible

version development

workflow runIterationWithNone {
    input {
        Array[String] outer_array = ["1", "2"]
        Boolean create_inner_array = false
    }

    if (create_inner_array) {
        scatter (count in ["one", "two"]) {
            call Echo as CreateArray {
                input:
                    non_optional_string=count
            }
        }
    }

    scatter (non_optional_string in outer_array) {
        scatter (optional_string in select_first([CreateArray.echo, [None]])) {
            call Echo as GetEcho {
                input:
                    non_optional_string=non_optional_string,
                    optional_string=optional_string
            }
        }
    }

    output {
        Array[String] echo = flatten(GetEcho.echo)
    }
}

task Echo {
    input {
        String non_optional_string
        String? optional_string
        # runtime
        String gatk_docker = "broadinstitute/gatk:4.0.0.0"
        Int? boot_disk_sizeGB = 12
        Int disk_spaceGB = 1
        Int memoryGB = 1
        Int command_memGB = 1
        Int? preemptible = 0
        Int? max_retries = 0
        Int cpu = 1
    }

    String string = non_optional_string + select_first([optional_string, ""])

    command <<<
        echo ~{string}
    >>>

    output {
        String echo = read_string(stdout())
    }

    runtime {
        docker: gatk_docker
        bootDiskSizeGb: boot_disk_sizeGB
        memory: memoryGB + " GB"
        disks: "local-disk " + disk_spaceGB + " HDD"
        preemptible: preemptible
        maxRetries: max_retries
        cpu: cpu
    }
}



Thanks!!
Best Regards
Jessa

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