etc/gatk-wdl/fm2/fm2.json

   1 {
   2         "fm2.sampleConfigFile": "fm2.samples.json",
   3         "fm2.bwaIndex": {
   4                 "fastaFile": "ref/ForensicM.fa.gz",
   5                 "indexFiles": [
   6                         "ref/ForensicM.fa.gz.sa",
   7                         "ref/ForensicM.fa.gz.amb",
   8                         "ref/ForensicM.fa.gz.ann",
   9                         "ref/ForensicM.fa.gz.bwt",
  10                         "ref/ForensicM.fa.gz.pac"
  11                 ]
  12         },
  13         "fm2.bwaThreads": 8,
  14         "fm2.minBWAmatchLen": 50,
  15         "fm2.dockerImagesFile": "dockerImages.yml"
  16 }