pathseq-pipeline.inputs.json

{
  "##_COMMENT1": "Inputs",
  "PathSeqPipelineWorkflow.input_bam": "gs://gatk-best-practices/pathseq/contaminated-bam/NA12878_24RG_med.hg380.7chicken0.3.bam",
  "PathSeqPipelineWorkflow.sample_name": "NA12878_24RG_med.hg380.7chicken0.3",

  "##_COMMENT1": "Reference and Resources",
  "PathSeqPipelineWorkflow.kmer_file": "gs://gatk-best-practices/pathseq/resources/pathseq_host.bfi",
  "PathSeqPipelineWorkflow.microbe_bwa_image": "gs://gatk-best-practices/pathseq/resources/meats.fa.img",
  "PathSeqPipelineWorkflow.microbe_fasta": "gs://gatk-best-practices/pathseq/resources/meats.fa",
  "PathSeqPipelineWorkflow.microbe_fasta_dict": "gs://gatk-best-practices/pathseq/resources/meats.dict",
  "PathSeqPipelineWorkflow.filter_bwa_image": "gs://gatk-best-practices/pathseq/resources/pathseq_host.fa.img",
  "PathSeqPipelineWorkflow.taxonomy_file": "gs://gatk-best-practices/pathseq/resources/meats.min2k.db",
  "PathSeqPipelineWorkflow.is_host_aligned": "false",

  "##_COMMENT1": "Docker",
  "PathSeqPipelineWorkflow.gatk_docker_override": "broadinstitute/gatk:4.0.11.0",
  "#PathSeqPipelineWorkflow.gatk4_jar_override": "File? (optional)",

  "##_COMMENT1": "Workflow options",
  "PathSeqPipelineWorkflow.filter_duplicates": "True",
  "#PathSeqPipelineWorkflow.min_clipped_read_length": "Int? (optional)",
  "#PathSeqPipelineWorkflow.filter_bwa_seed_length": "Int? (optional)",
  "#PathSeqPipelineWorkflow.min_score_identity": "Float? (optional)",
  "#PathSeqPipelineWorkflow.host_min_identity": "Int? (optional)",
  "#PathSeqPipelineWorkflow.PathseqPipeline.skip_quality_filters": "Boolean? (optional)",
  "#PathSeqPipelineWorkflow.PathseqPipeline.default_min_score_identity": "Float (optional, default = 0.9)",
  "#PathSeqPipelineWorkflow.identity_margin": "Float? (optional)",
  "#PathSeqPipelineWorkflow.skip_pre_bwa_repartition": "Boolean? (optional)",
  "PathSeqPipelineWorkflow.divide_by_genome_length": "True",
  "#PathSeqPipelineWorkflow.bam_partition_size": "Int? (optional)",
  "#PathSeqPipelineWorkflow.PathseqPipeline.default_identity_margin": "Float (optional, default = 0.02)",
  "#PathSeqPipelineWorkflow.PathseqPipeline.default_ram_mb": "Int (optional, default = 208000)",

  "##_COMMENT1": "Runtime Parameter",
  "#PathSeqPipelineWorkflow.mem_gb": "Int? (optional)",
  "#PathSeqPipelineWorkflow.cpu": "Int? (optional)",
  "#PathSeqPipelineWorkflow.increase_disk_size": "Int? (optional)",
  "#PathSeqPipelineWorkflow.PathseqPipeline.default_disk_space_gb": "Float (optional, default = 400.0)",
  "#PathSeqPipelineWorkflow.PathseqPipeline.use_ssd": "Boolean (optional, default = true)",
  "#PathSeqPipelineWorkflow.preemptible_attempts": "Int? (optional)"
}