etc/gatk-wdl/fm2gatk/fm2.json

   1 {
   2         "Germline.sampleConfigFile": "fm2.csv",
   3         "Germline.referenceFasta": "/share/FGI2017B/users/huxs/2020Q4_fm2/ref/Homo_sapiens_assembly38.fasta.gz",
   4         "Germline.referenceFastaFai": "/share/FGI2017B/users/huxs/2020Q4_fm2/ref/Homo_sapiens_assembly38.fasta.gz.fai",
   5         "Germline.referenceFastaDict": "/share/FGI2017B/users/huxs/2020Q4_fm2/ref/Homo_sapiens_assembly38.dict",
   6         "Germline.bwaIndex": {
   7                 "fastaFile": "/share/FGI2017B/users/huxs/2020Q4_fm2/ref/Homo_sapiens_assembly38.fasta.gz",
   8                 "indexFiles": [
   9                         "/share/FGI2017B/users/huxs/2020Q4_fm2/ref/Homo_sapiens_assembly38.fasta.gz.sa",
  10                         "/share/FGI2017B/users/huxs/2020Q4_fm2/ref/Homo_sapiens_assembly38.fasta.gz.amb",
  11                         "/share/FGI2017B/users/huxs/2020Q4_fm2/ref/Homo_sapiens_assembly38.fasta.gz.ann",
  12                         "/share/FGI2017B/users/huxs/2020Q4_fm2/ref/Homo_sapiens_assembly38.fasta.gz.bwt",
  13                         "/share/FGI2017B/users/huxs/2020Q4_fm2/ref/Homo_sapiens_assembly38.fasta.gz.pac"
  14                 ]
  15         },
  16         "Germline.dockerImagesFile": "dockerImages.yml",
  17         "Germline.dbsnpVCF": "/share/FGI2017B/users/huxs/2020Q4_fm2/20210323/ref/dbsnp154.vcf.gz",
  18         "Germline.dbsnpVCFIndex": "/share/FGI2017B/users/huxs/2020Q4_fm2/gatk/ref/dbsnp154.vcf.gz.tbi",
  19         "Germline.regions###": "File? (optional)",
  20         "Germline.jointgenotyping": "false",
  21         "Germline.singleSampleGvcf": "true",
  22         "Germline.adapterForward": "AAGTCGGAGGCCAAGCGGTCTTAGGAAGACAA",
  23         "Germline.adapterReverse": "AAGTCGGATCGTAGCCATGTCGTTC",
  24         "Germline.useBwaKit###": "Boolean (optional, default = false)",
  25         "Germline.runSVcalling###": "Boolean (optional, default = false)",
  26         "Germline.outputDir###": "String (optional, default = \".\")",
  27         "Germline.sampleWorkflow.metrics.ampliconIntervals###": "File? (optional)",
  28         "Germline.sampleWorkflow.metrics.targetIntervals###": "Array[File]+? (optional)",
  29         "Germline.SingleSampleCalling.dontUseSoftClippedBases###": "Boolean (optional, default = false)"
  30 }