bam-fastq.json

{
  "##_COMMENT0": "INPUT/OUTPUT BAM",
  "BamToFastq.input_bams_file": "gs://neurogap/high_coverage/WGS/neurogap.sample_bam2",

  "##_COMMENT5": "DOCKERS",
  "#BamToFastq.gatk_docker_override": "String? (optional)",

  "##_COMMENT6": "PATHS",
  "#BamToFastq.gatk_path_override": "String? (optional)",

  "##_COMMENT7": "JAVA OPTIONS",
  "#BamToFastq.HaplotypeCaller.java_options": "String? (optional)",

  "##_COMMENT8": "MEMORY ALLOCATION",
  "#BamToFastq.HaplotypeCaller.mem_gb": "Int? (optional)",
  "#BamToFastq.MergeGVCFs.mem_gb": "Int? (optional)",
  "#BamToFastq.CramToBamTask.machine_mem_gb": "Int? (optional)",

  "##_COMMENT9": "DISK SIZE ALLOCATION",
  "#BamToFastq.HaplotypeCaller.disk_space_gb": "Int? (optional)",
  "#BamToFastq.MergeGVCFs.disk_space_gb": "Int? (optional)",
  "#BamToFastq.CramToBamTask.disk_space_gb": 300,

  "##_COMMENT10": "PREEMPTION",
  "#BamToFastq.HaplotypeCaller.preemptible_attempts": "Int? (optional)",
  "#BamToFastq.MergeGVCFs.preemptible_attempts": "Int? (optional)",
  "#BamToFastq.CramToBamTask.preemptible_attempts": 4
}