Looks like parameter file needs update past 2.0.3

[denis-yuen]

{
  "reference": {
    "path": "/path/to/core_ref_GrCh38.tar.gz",
    "class": "File"
  },
  "bwa_idx": {
    "path": "/path/to/bwa_idx_GrCh38.tar.gz",
    "class": "File"
  },
  "sample": "sim",
  "seq_in": [
    {
      "path": "/path/to/read_1.fastq",
      "class": "File"
    },
    {
      "path": "/path/to/read_2.fastq",
      "class": "File"
    }
  ],
  "out_bam": {
    "path": "/path/to/mapped.bam",
    "class": "File"
  },
  "bwa": " -Y -K 100000000",
  "mmqc": false,
  "mmqcfrac": 0.05
}

See conversation at https://gitter.im/ga4gh/dockstore?at=5d8beae234a7236bf5bef131

[byb121]

Checked. We have the correct example files on Dockstore website and in this repo. We'll need someone to point us to the wrong example.

[keiranmraine]

Currently reorganising the base code from the CWL+helpers. Should be a new release soon and will confirm all examples are working as expected during this cycle.