dxapp.json

{
  "name": "eggd_athena",
  "title": "eggd_athena",
  "summary": "DNAnexus app of Athena",
  "dxapi": "1.0.0",
  "version": "1.5.0",
  "properties": {
    "githubRelease": "v1.5.0",
    "athenaRelease": "v1.5.0"
    },
  "authorizedUsers": [
      "org-emee_1",
      "user-jethror1",
      "user-spaul4"
  ],
  "developers": [
      "org-emee_1",
      "user-jethror1",
      "user-spaul4"
  ],
  "inputSpec": [
    {
      "name": "panel_bed",
      "label": "BED file of panel",
      "class": "file",
      "optional": false,
      "patterns": [
        "*.bed"
      ],
      "help": ""
    },
    {
      "name": "exons_file",
      "label": "Exons file defining gene names and exon numbers for all transcripts / regions (from 001_References)",
      "class": "file",
      "optional": false,
      "suggestions": [
        {
          "project": "project-Fkb6Gkj433GVVvj73J7x8KbV",
          "path": "/annotation/b37/"
        }
      ],
      "patterns": [
        "*"
      ],
      "help": ""
    },
    {
      "name": "mosdepth_files",
      "label": "Array of files output from mosdepth.",
      "class": "array:file",
      "optional": false,
      "patterns": [
        "*"
      ],
      "help": "Array of eggd_mosdepth output files, uses per base bed and reference build txt file."
    },
    {
        "name": "per_chromosome_coverage",
        "label": "Include per-chromosome coverage plots.",
        "class": "boolean",
        "default": false,
        "help": ""
    },
    {
      "name": "thresholds",
      "label": "String of comma seperated thresholds at which to calculate coverage",
      "class": "string",
      "optional": true,
      "default": "10, 20, 30, 50, 100",
      "help": ""
    },
    {
      "name": "cutoff_threshold",
      "label": "Threshold to define sub-optimal coverage",
      "class": "int",
      "optional": true,
      "default": 20,
      "help": ""
    },
    {
      "name": "name",
      "label": "Sample name, used in report and for naming output files",
      "class": "string",
      "optional": true,
      "help": ""
    },
    {
      "name": "limit",
      "label": "Number of genes at which to skip full gene plot generation, for large panels this may take a long time.",
      "class": "int",
      "optional": true,
      "default": -1,
      "help": ""
    },
    {
      "name": "panel",
      "label": "Display panel",
      "class": "boolean",
      "default": true,
      "help": "Display panel(s) / gene(s) from name of panel bed file. Default: True"
    },
    {
      "name": "panel_filters",
      "label": "panel filters",
      "class": "string",
      "help": "Drop down gene panel filters for full gene plots, should be given as panel1:gene1,gene2,gene3"
    },
    {
      "name": "snps",
      "label": "SNP VCFs to check coverage for",
      "class": "array:file",
      "optional": true,
      "patterns": [
        "*.vcf*"
      ],
      "help": ""
    },
    {
      "name": "summary",
      "label": "Report summary",
      "class": "boolean",
      "default": false,
      "help": "Display summary of genes / transcripts in report in summary section. Default: False"
    }
  ],
  "outputSpec": [
    {
      "name": "exon_stats",
      "label": "Exon statistics file",
      "class": "file",
      "patterns": [
        "*"
      ],
      "help": ""
    },
    {
      "name": "gene_stats",
      "label": "Gene statistics file",
      "class": "file",
      "patterns": [
        "*"
      ],
      "help": ""
    },
    {
      "name": "report",
      "label": "HTML coverage report",
      "class": "file",
      "patterns": [
        "*"
      ],
      "help": ""
    },
    {
      "name": "annotated_bed",
      "label": "Annotated BED file",
      "class": "file",
      "patterns": [
        "*"
      ],
      "help": ""
    }
  ],
  "runSpec": {
    "timeoutPolicy": {
      "*": {
        "hours": 4
      }
    },
    "interpreter": "bash",
    "file": "src/eggd_athena.sh",
    "distribution": "Ubuntu",
    "release": "20.04",
    "version": "0"
  },
  "access": {
    "project": "CONTRIBUTE"
  },
  "regionalOptions": {
    "aws:eu-central-1": {
      "systemRequirements": {
        "*": {
          "instanceType": "mem1_ssd1_v2_x16"
        }
      }
    }
  }
}