dxapp.json

{
  "name": "mrcepid-collecthsmetrics",
  "title": "CollectHsMetrics",
  "summary": "Calculates coverage stats for a single CRAM file based on a set of input intervals",
  "dxapi": "1.0.0",
  "version": "0.0.2",
  "openSource": true,
  "inputSpec": [
    {
      "name": "cram_list",
      "label": "List of cram files to process in this instance",
      "class": "file",
      "optional": false,
      "patterns": [
        "*.txt"
      ],
      "help": ""
    },
    {
      "name": "intervals",
      "label": "Interval array in GATK/Picard interval format",
      "class": "array:file",
      "optional": false,
      "patterns": [
        "*.interval_list"
      ],
      "help": ""
    },
    {
      "name": "threads",
      "label": "number of threads available to this instance",
      "class": "int",
      "optional": true,
      "default": 16,
      "help": "Number of threads available to this instance."
    },
    {
      "name": "output_file",
      "label": "File to output results to. Default name is coverage.txt.gz",
      "class": "string",
      "optional": true,
      "default": "coverage.txt.gz",
      "patterns": [
        "*.txt.gz"
      ],
      "help": ""
    }
  ],
  "outputSpec": [
    {
      "name": "output_file",
      "label": "Output file with coverage stats",
      "class": "file",
      "optional": false,
      "patterns": [
        "*.gz"
      ],
      "help": ""
    }
  ],
  "runSpec": {
    "timeoutPolicy": {
      "*": {
        "hours": 80
      }
    },
    "interpreter": "python3",
    "file": "src/mrcepid-collecthsmetrics.py",
    "distribution": "Ubuntu",
    "release": "20.04",
    "version": "0",
    "execDepends": [
      {"name": "openjdk-8-jre-headless"}
    ]
  },
  "regionalOptions": {
    "aws:eu-west-2": {
      "systemRequirements": {
        "*": {
          "instanceType": "mem3_ssd1_v2_x16"
        }
      }
    }
  }
}