We're writing a workflow where we process a couple of bams separately, then run processes with them together (DNAseq somatic). The workflows scatter the tumor/normal for parallel processing, ending up with "tumor.sorted.bam" and "normal.sorted.bam", then gather them for a realignments step in an array with an output of "tumor.realigned.bam" and "normal.realigned.bam". (BAM index files (*.bai) are created and passed along as secondaryFiles for each of these steps here and below as apppropriate)

These bams need some post-processing (resort, dealing with duplicate reads), and I'm able to scatter those bams and get "tumor.realigned.md.bam" and "normal.realigned.md.bam" back as what I believe to be an array of Files.

In the next step, I try to run and ExpressionTool to convert the array of Files into two File objects with secondaryFiles so I can refer to the tumor and normal bams explictly, but I think something is failing in my JavaScript ExpressionTool.

class: ExpressionTool
# collect_tumor_normal_bams.cwl
cwlVersion: v1.0
inputs:
  bams:
    type: File[]
    secondaryFiles: [".bai"]
outputs:
  tumorBam: File
  normalBam: File
requirements:
  InlineJavascriptRequirement: {}
expression: |
  ${

    var tumor = [];
    var tumorSecondary = [];
    var normal = [];
    var normalSecondary = [];

    for (var filenum in inputs.bams) {
      if (inputs.bams[filenum].basename.match(/tumor[^\/]*\.bam$/i) ) {
        tumor.push (inputs.bams[filenum]);
      }
      if (inputs.bams[filenum].basename.match(/tumor[^\/]*\.bai$/i)) {
        tumorSecondary.push (inputs.bams[filenum]);
      }

      if (inputs.bams[filenum].basename.match(/normal[^\/]*\.bam$/i)) {
        normal.push (inputs.bams[filenum]);
      }
      if (inputs.bams[filenum].basename.match(/normal[^\/]*\.bai$/i)) {
        normalSecondary.push (inputs.bams[filenum]);
      }

    }

    tumor["secondaryFiles"] = tumorSecondary;
    normal["secondaryFiles"] = normalSecondary;

    return {"tumorBam": tumor, "normalBam": normal}
    }

Here is a snippet from the higher-level CWL that is calling the above:

# lots of stuff above here that works
  realign:
     run: commandline/realign.cwl
     in:
       bam_files: stageForRealign/bamFiles
       reference_fasta: referenceFasta
       targets_bed: captureBed
     out:
       [bam_file]

   post_realign_sort_index_md:
     run: commandline/bamSortMarkDups.cwl
     scatter: input_file
     in:
       input_file: realign/bam_file
     out:
       [bam_file]

   # Everything works above here:  I get the expected BAMs and BAIs
   # nothing below here works:  I suspect this is an issue with my ExpressionTool, 
   # but I don't know a good way to debug

   collectTN:
     run: expression/collect_tumor_normal_bams.cwl
     in:
       bams: [post_realign_sort_index_md/bam_file]
     out:
       [tumorBam, normalBam]

   coverage_tumor:
     run: commandline/coverage.cwl
     in: 
       bam_file: collectTN/tumorBam
       bed_file: coverageWindows
       genome_file: bedtoolsGenome
     out:
       [counts_file]

   coverage_normal:
     run: commandline/coverage.cwl
     in: 
       bam_file: collectTN/normalBam
       bed_file: coverageWindows
       genome_file: bedtoolsGenome
     out:
       [counts_file]

   call_somatic_variants: 
     run: commandline/somatic-caller.cwl
     in: 
       tumor_bam_file: collectTN/tumorBam
       normal_bam_file: collectTN/normalBam
       reference_fasta: referenceFasta
       regions_bed: captureBed 
     out: 
      [ somatic_caller_output ]

If it makes a difference, we're using the Arvados CWL runner.