Inputs are duplicated in generated TES task message

[adamstruck]

A single input is mapped to two entries in the TES message.

CWL:

cwlVersion: v1.0
class: CommandLineTool
doc: "Invoke 'samtools index' to create a 'BAI' index"

requirements:
  - class: DockerRequirement
    dockerPull: biocontainers/samtools:latest
  - class: InitialWorkDirRequirement
    listing: [ $(inputs.alignments) ]

inputs:
  alignments:
    type: File
    inputBinding:
      position: 1
      valueFrom: $(self.basename)
    label: Input bam file.

outputs:
  alignments_with_index:
    type: File
    secondaryFiles: .bai
    outputBinding:
      glob: $(inputs.alignments.basename)

baseCommand: ["samtools", "index"]

Inputs JSON:

{
  "alignments": {
    "location": "s3://s3.us-west-2.amazonaws.com/funnel-test/NA12878.bam",
    "class": "File"
  }
}

Resulting TES Task:

{
  "id": "b9f2psnpbjg715qbbnr0",
  "state": "COMPLETE",
  "name": "root.index",
  "inputs": [
    {
      "name": "NA12878.bam",
      "url": "s3://s3.us-west-2.amazonaws.com/funnel-test/NA12878.bam",
      "path": "/Users/strucka/scratch/cwl/samtools/inputs/257cbe72-9f3a-469b-b925-c63dd39e46d3/root/index/NA12878.bam"
    },
    {
      "name": "NA12878.bam",
      "url": "s3://s3.us-west-2.amazonaws.com/funnel-test/NA12878.bam",
      "path": "/funnel-test/NA12878.bam"
    }
  ],
  "outputs": [
    {
      "name": "index",
      "url": "s3://s3.us-west-2.amazonaws.com/funnel-test/bunny/257cbe72-9f3a-469b-b925-c63dd39e46d3/root/index",
      "path": "/Users/strucka/scratch/cwl/samtools/inputs/257cbe72-9f3a-469b-b925-c63dd39e46d3/root/index",
      "type": "DIRECTORY"
    }
  ],
  "resources": {

  },
  "executors": [
    {
      "image": "biocontainers/samtools:latest",
      "command": [
        "/bin/sh",
        "-c",
        "samtools index NA12878.bam"
      ],
      "workdir": "/Users/strucka/scratch/cwl/samtools/inputs/257cbe72-9f3a-469b-b925-c63dd39e46d3/root/index",
      "stderr": "/Users/strucka/scratch/cwl/samtools/inputs/257cbe72-9f3a-469b-b925-c63dd39e46d3/root/index/job.err.log",
      "env": {
        "HOME": "/Users/strucka/scratch/cwl/samtools/inputs/257cbe72-9f3a-469b-b925-c63dd39e46d3/root/index",
        "TMPDIR": "/Users/strucka/scratch/cwl/samtools/inputs/257cbe72-9f3a-469b-b925-c63dd39e46d3/root/index"
      }
    }
  ],
}

[adamstruck]

This appears to be due to the InitialWorkDirRequirement of this CWL CommandLineTool.