etc/gatk-wdl/germline1-haplotypecaller-gvcf-gatk4.hg38.wgs.inputs.json

   1 {
   2   "##_COMMENT1": "INPUT BAM",
   3   "HaplotypeCallerGvcf_GATK4.input_bam": "/share/FGI2017B/users/huxs/nsfcG/wgs/WGS-D3B.hg38.bam",
   4   "HaplotypeCallerGvcf_GATK4.input_bam_index": "/share/FGI2017B/users/huxs/nsfcG/wgs/WGS-D3B.hg38.bai",
   5   "#HaplotypeCallerGvcf_GATK4.input_bam": "gs://broad-public-datasets/NA12878/NA12878.cram",
   6   "#HaplotypeCallerGvcf_GATK4.input_bam_index": "gs://broad-public-datasets/NA12878/NA12878.cram.crai",
   7
   8   "##_COMMENT2": "REFERENCE FILES",
   9   "HaplotypeCallerGvcf_GATK4.ref_dict": "/hwfssz1/pub/database/storage.googleapis.com/broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
  10   "HaplotypeCallerGvcf_GATK4.ref_fasta": "/hwfssz1/pub/database/storage.googleapis.com/broad-references/hg38/v0/Homo_sapiens_assembly38.fasta",
  11   "HaplotypeCallerGvcf_GATK4.ref_fasta_index": "/hwfssz1/pub/database/storage.googleapis.com/broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
  12
  13   "##_COMMENT3": "INTERVALS, https://console.cloud.google.com/storage/browser/gatk-test-data/intervals/",
  14   "HaplotypeCallerGvcf_GATK4.scattered_calling_intervals_list": "/share/FGI2017B/pub/Ref/gatk-test-data/intervals/local_hg38_wgs_scattered_calling_intervals.txt",
  15
  16   "##_COMMENT4": "MISCELLANEOUS PARAMETERS",
  17   "#HaplotypeCallerGvcf_GATK4.HaplotypeCaller.make_gvcf": "True",
  18   "#HaplotypeCallerGvcf_GATK4.HaplotypeCaller.contamination": "Float? (optional)",
  19
  20   "##_COMMENT5": "DOCKERS",
  21   "#HaplotypeCallerGvcf_GATK4.gatk_docker_override": "String? (optional)",
  22   "#HaplotypeCallerGvcf_GATK4.gitc_docker_override": "String? (optional)",
  23
  24   "##_COMMENT6": "PATHS",
  25   "#HaplotypeCallerGvcf_GATK4.gatk_path_override": "String? (optional)",
  26
  27   "##_COMMENT7": "JAVA OPTIONS",
  28   "#HaplotypeCallerGvcf_GATK4.HaplotypeCaller.java_options": "String? (optional)",
  29
  30   "##_COMMENT8": "MEMORY ALLOCATION",
  31   "#HaplotypeCallerGvcf_GATK4.HaplotypeCaller.mem_gb": "Int? (optional)",
  32   "#HaplotypeCallerGvcf_GATK4.MergeGVCFs.mem_gb": "Int? (optional)",
  33   "#HaplotypeCallerGvcf_GATK4.CramToBamTask.machine_mem_gb": "Int? (optional)",
  34
  35   "##_COMMENT9": "DISK SIZE ALLOCATION",
  36   "#HaplotypeCallerGvcf_GATK4.HaplotypeCaller.disk_space_gb": "Int? (optional)",
  37   "#HaplotypeCallerGvcf_GATK4.MergeGVCFs.disk_space_gb": "Int? (optional)",
  38   "#HaplotypeCallerGvcf_GATK4.CramToBamTask.disk_space_gb": "Int? (optional)",
  39
  40   "##_COMMENT10": "PREEMPTION",
  41   "#HaplotypeCallerGvcf_GATK4.HaplotypeCaller.preemptible_attempts": "Int? (optional)",
  42   "#HaplotypeCallerGvcf_GATK4.MergeGVCFs.preemptible_attempts": "Int? (optional)",
  43   "#HaplotypeCallerGvcf_GATK4.CramToBamTask.preemptible_attempts": "Int? (optional)"
  44 }