pathogenome-amr-detection/nextflow_schema.json at main · caporaso-lab/pathogenome-amr-detection · GitHub

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{
  "$schema": "http://json-schema.org/draft-07/schema",
  "title": "Pathogenome workflow parameters",
  "description": "Parameters for downloading accession reads, assembling contigs, predicting genes, and annotating antimicrobial resistance.",
  "type": "object",
  "required": [
    "accessions",
    "fondue_email"
  ],
  "properties": {
    "accessions": {
      "type": "string",
      "format": "file-path",
      "mimetype": "text/tsv",
      "title": "Accession IDs",
      "description": "TSV file with a sample-id header and one NCBI or ENA run accession per row."
    },
    "fondue_email": {
      "type": "string",
      "format": "email",
      "title": "Contact email",
      "description": "Email address supplied to q2-fondue for accession downloads."
    },
    "import_threads": {
      "type": "integer",
      "minimum": 1,
      "default": 1,
      "title": "Accession import CPUs",
      "description": "Number of CPUs allocated to the accession import step."
    },
    "import_memory_gb": {
      "type": "integer",
      "minimum": 1,
      "default": 8,
      "title": "Accession import memory (GB)",
      "description": "Memory allocated to the accession import step, in GB."
    },
    "import_time_hours": {
      "type": "integer",
      "minimum": 1,
      "default": 1,
      "title": "Accession import time limit (hours)",
      "description": "Maximum runtime for the accession import step, in hours."
    },
    "fondue_threads": {
      "type": "integer",
      "minimum": 1,
      "default": 8,
      "title": "Fondue threads",
      "description": "Number of download threads and CPUs used by q2-fondue."
    },
    "fondue_memory_gb": {
      "type": "integer",
      "minimum": 1,
      "default": 16,
      "title": "Fondue memory (GB)",
      "description": "Memory allocated to the read download step, in GB."
    },
    "fondue_time_hours": {
      "type": "integer",
      "minimum": 1,
      "default": 36,
      "title": "Fondue time limit (hours)",
      "description": "Maximum runtime for the read download step, in hours."
    },
    "megahit_threads": {
      "type": "integer",
      "minimum": 1,
      "default": 12,
      "title": "MEGAHIT threads",
      "description": "Number of assembly threads and CPUs used by MEGAHIT."
    },
    "megahit_memory_gb": {
      "type": "integer",
      "minimum": 1,
      "default": 64,
      "title": "MEGAHIT memory (GB)",
      "description": "Memory allocated to the assembly step, in GB."
    },
    "megahit_time_hours": {
      "type": "integer",
      "minimum": 1,
      "default": 48,
      "title": "MEGAHIT time limit (hours)",
      "description": "Maximum runtime for the assembly step, in hours."
    },
    "prodigal_threads": {
      "type": "integer",
      "minimum": 1,
      "default": 12,
      "title": "Prodigal CPUs",
      "description": "Number of CPUs allocated to the gene prediction step."
    },
    "prodigal_memory_gb": {
      "type": "integer",
      "minimum": 1,
      "default": 32,
      "title": "Prodigal memory (GB)",
      "description": "Memory allocated to the gene prediction step, in GB."
    },
    "prodigal_time_hours": {
      "type": "integer",
      "minimum": 1,
      "default": 24,
      "title": "Prodigal time limit (hours)",
      "description": "Maximum runtime for the gene prediction step, in hours."
    },
    "amr_db_threads": {
      "type": "integer",
      "minimum": 1,
      "default": 8,
      "title": "AMRFinderPlus database CPUs",
      "description": "Number of CPUs allocated to the AMRFinderPlus database download step."
    },
    "amr_db_memory_gb": {
      "type": "integer",
      "minimum": 1,
      "default": 16,
      "title": "AMRFinderPlus database memory (GB)",
      "description": "Memory allocated to the AMRFinderPlus database download step, in GB."
    },
    "amr_db_time_hours": {
      "type": "integer",
      "minimum": 1,
      "default": 24,
      "title": "AMRFinderPlus database time limit (hours)",
      "description": "Maximum runtime for the AMRFinderPlus database download step, in hours."
    },
    "amr_threads": {
      "type": "integer",
      "minimum": 1,
      "default": 4,
      "title": "AMR annotation threads",
      "description": "Number of threads and CPUs used by AMRFinderPlus annotation."
    },
    "amr_memory_gb": {
      "type": "integer",
      "minimum": 1,
      "default": 128,
      "title": "AMR annotation memory (GB)",
      "description": "Memory allocated to the AMRFinderPlus annotation step, in GB."
    },
    "amr_time_hours": {
      "type": "integer",
      "minimum": 1,
      "default": 24,
      "title": "AMR annotation time limit (hours)",
      "description": "Maximum runtime for the AMRFinderPlus annotation step, in hours."
    }
  }
}