Update: July 26, 2019
This section of the forum is now closed; we are working on a new support model for WDL that we will share here shortly. For Cromwell-specific issues, see the Cromwell docs and post questions on Github.

Can't use named inputs


I'm trying to run CombineVariants as part of a WDL workflow. I'm interested in providing the recommended tag names for my inputs in order to use priority argument. However, I can't figure out a way to do this properly in WDL.

Let's say I have inputs in a data structure like this:

Array[String] priority = [
Array[File] input_variants = [

Now I want to write a command that looks like:

${java_path} -Xms${memory}m -jar ${gatk_path} \
    --analysis_type  CombineVariants \
    --num_threads ${threads} \
    --reference_sequence ${reference} \
    --genotypemergeoption PRIORITIZE \
    --rod_priority_list ${sep="," priority} \
    --variant:HaplotypeCaller /path/to/cromwell/mapped/inputs/.../UtahProband.haplotype_caller.vcf.gz --variant:Samtools /path/to/cromwell/mapped/inputs/.../UtahProband.samtools.vcf.gz \
    --out ${output_file_prefix}.vcf.gz

Is there a way to get this in WDL? Ideally, while still getting to declare inputs as proper File type so that Cromwell will know to localize the File inputs. I know I could build an array of strings in the workflow calling the task and then use "sep", but that's not ideal. Any other clever way to accomplish this?


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