Run NEON sample end to end in Dev

[mbthornton-lbl]

Start with the following Data Gen ID:
test 1 (from before the Jan NERSC maintenance): nmdc:omprc-11-hcjd7y28
test 2: nmdc:omprc-11-rejajm76
test 3: nmdc:omprc-11-qww9t685

If more test IDs are needed used the next record from this aggregation query:

db.getCollection('data_generation_set').aggregate(
  [
    {
      $match: {
        associated_studies:
          'nmdc:sty-11-34xj1150',
        analyte_category: 'metagenome'
      }
    },
    {
      $lookup: {
        from: 'workflow_execution_set',
        localField: 'id',
        foreignField: 'was_informed_by',
        as: 'workflow_execution_set'
      }
    },
    {
      $lookup: {
        from: 'data_object_set',
        localField: 'has_output',
        foreignField: 'id',
        as: 'do_output'
      }
    },
    {
      $match: {
        'do_output.in_manifest': {
          $exists: false
        }
      }
    },
    {
      $match: {
        workflow_execution_set: { $size: 0 }
      }
    }
  ],
  { maxTimeMS: 60000, allowDiskUse: true }
);

[aclum]

@mbthornton-lbl this failed, there is no output directory. cromwell run directory is 41ec9955-f8b4-4676-86c3-f2714a67b016

[aclum]

Root cause is mismatching input key names between the wdl and the workflows.yaml