Method configuration to access sample attribute values in sample set

akmanningakmanning United StatesMember

I am configuring a method for a sample set.

In my data model, my samples have an attribute called clean_results_file, and I would like to access these attribute values for all samples in a sample set. I have the following WDL which works with Cromwell with a file (my_cleanfiles) that lists each input clean_result_file.

Root entity type: sample_set

    workflow workflowmeta {

    File my_cleanfiles

    Array[File] cleanfiles = read_lines(my_cleanfiles)


What is the appropriate way get the Array[File] cleanfiles to contain the clean_result_files attribute in FireCloud?

I was trying "workflowmeta.my_cleanfiles: (File) this.samples.clean_results_file" Does this method configuration create an Array[File]?


Best Answer


  • abaumannabaumann Broad DSDEMember, Broadie ✭✭✭

    Yes, your answer would be correct for use in FireCloud. Make an array in the WDL and pass the value to the WDL using an expression in your method configuration (e.g. running on a sample set you can have this.samples.bam which will make an array of each sample's BAM file in the sample set)

    We are in the process of adding support for array literals in FireCloud method configurations so you could write for instance ["gs://some_bucket/some_file.bam", "gs://some_bucket/some_other_file.bam"] rather than only being able to build them from a set.

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