test_wdl_config.json

{
  "jumping_tortoise.pathToReference": "/path/to/reference_tarball/reference.tar.bz2",
  "jumping_tortoise.reference": "reference.fa",  
  "jumping_tortoise.sample_suffix": "_supersmall.bam",
  "jumping_tortoise.glnexus_ram_hc": 150,
  "jumping_tortoise.glnexus_ram_dv": 150,
  "jumping_tortoise.cram_files": [
  [
    {
      "cram": "/path/toNA12891_supersmall.bam",
      "crai": "/path/toNA12891_supersmall.bam.bai"
    },
    {
      "cram": "/path/toNA12892_supersmall.bam",
      "crai": "/path/toNA12892_supersmall.bam.bai"
    },
    {
      "cram": "/path/toNA12878_supersmall.bam",
      "crai": "/path/toNA12878_supersmall.bam.bai"
    }
  ]
  ],
  "jumping_tortoise.naive_inheritance_trio_py2":"/path/to/naive_inheritance_trio_py2.py",
  "jumping_tortoise.test_intersect":"/path/to/test_intersect.py",
  "jumping_tortoise.filter_glnexuscombined_updated":"/path/to/filter_glnexuscombined_updated.py",
  "jumping_tortoise.trios":[
  {
    "father" :"NA12891",
    "mother": "NA12892",
    "child": "NA12878"
  }
  ],
  "jumping_tortoise.regions": "/path/to/regions.tar.bz2"
}