dxapp.json

{
  "name": "vcfeval_hap.py_v1.4.3",
  "summary": "v1.4.3 - Use vcfeval and hap.py to calculate NGS performance metrics against truth set (based on precisionFDA app)",
  "properties": {
    "github release": "v1.4.3"
  },
  "dxapi": "1.0.0",
  "inputSpec": [
    {
      "name": "query_vcf",
      "label": "Query VCF",
      "help": "VCF file containing queryset variants (.vcf or .vcf.gz)",
      "class": "file",
      "patterns": ["*.vcf", "*.vcf.gz"]
    },
    {
      "name": "truth_vcf",
      "label": "Truth VCF",
      "help": "VCF file containing truthset variants (.vcf or .vcf.gz)",
      "class": "file",
      "patterns": ["*.vcf", "*.vcf.gz"]
    },
    {
      "name": "panel_bed",
      "label": "Panel BED",
      "help": "BED containing region (e.g. panel) covered in queryset vcf",
      "class": "file",
      "patterns": ["*.bed"]
    },
    {
      "name": "high_conf_bed",
      "label": "High Confidence BED",
      "help": "BED containing high confidence region for truth set",
      "class": "file",
      "patterns": ["*.bed"]
    },
    {
      "name": "prefix",
      "label": "Output prefix",
      "class": "string",
      "optional": false
    },
    {
      "name": "na12878",
      "label": "Perform NA12878 stratification? (SEE README)",
      "help": "If the truth set is NA12878, stratification of results will be performed. However this requires the instance type to be upgraded to at least 7GB of RAM and will take longer.",
      "class": "boolean",
      "default": false
    },
    {
      "name": "genome_reference",
      "class": "string",
      "default": "GRCh37",
      "choices": [
        "GRCh37",
        "GRCh38"
      ]
    },
    {
      "name": "skip",
      "label": "skip",
      "help": "Skip this step if not required",
      "class": "boolean",
      "optional": false,
      "default": false
    }
  ],
  "outputSpec": [
    {
      "name": "detailed_results",
      "label": "Archive with detailed results",
      "class": "file",
      "optional": true
    },
    {
      "name": "summary_csv",
      "label": "Summary CSV",
      "class": "file",
      "optional": true
    },
    {
      "name": "summary_html",
      "label": "Summary HTML report",
      "class": "file",
      "optional": true
    }
  ],
  "runSpec": {
    "interpreter": "bash",
    "headJobOnDemand": false,
    "execDepends": [
      {
        "name": "tabix",
        "version": "1.10.2-3"
      }
    ],
    "distribution": "Ubuntu",
    "release": "20.04",
    "version": "0",
    "file": "src/code.sh"
  },
  "access": {
    "network": [
      "*"
    ],
    "allProjects": "VIEW"
  },
  "ignoreReuse": false,
  "regionalOptions": {
    "aws:us-east-1": {
      "systemRequirements": {
        "*": {
          "instanceType": "mem1_ssd1_v2_x2"
        }
      }
    }
  }
}