dxapp.json

{
  "name": "eggd_mosdepth",
  "title": "eggd_mosdepth_v1.1.0",
  "version": "1.1.0",
  "whatsNew": "* v1.1.0 Uses samtools v1.18 as an asset and mosdepth docker as an input, updated app name and runSpec.",
  "summary": "Runs mosdepth to perform coverage analysis",
  "dxapi": "1.0.0",
  "properties": {
  "githubRelease": "v1.1.0"
  },
  "inputSpec": [
    {
      "name": "optional_arguments",
      "label": "optional args",
      "class": "string",
      "optional": true,
      "help": "optional arguments as described in the docs: https://github.com/brentp/mosdepth."
    },
    {
      "name": "quantize_labels",
      "label": "optional quantize labels",
      "class": "string",
      "optional": true,
      "help": "List of comma seperated labels for bins if using --quantize, number of labels must match number of bins. If none are given the defaults from the readme are passed."
    },
    {
      "name": "bam",
      "label": "BAM file",
      "class": "file",
      "optional": false,
      "patterns": [
        "*.bam$"
      ],
      "help": "BAM file to generate bp coverage on"
    },
    {
      "name": "index",
      "label": "Index file",
      "class": "file",
      "optional": false,
      "patterns": [
        "*.bai$"
      ],
      "help": "Index of BAM"
    },
    {
      "name": "bed",
      "label": "bed file",
      "class": "file",
      "optional": true,
      "patterns": [
        ".bed$"
      ],
      "help": "BED file to generate regions.bed"
    },
    {
      "name": "qual_flags",
      "label": "Quality flags",
      "class": "boolean",
      "default": true,
      "help": "Optional remove duplicate and multi mapped reads using --flag 1796 --mapq 20. Default: True"
    },
    {
      "name": "mosdepth_docker",
      "label": "Mosdepth Docker",
      "help": "compressed image of Mosdepth Docker",
      "optional": false,
      "class": "file",
      "patterns": ["*.tar.gz"],
      "suggestions": [
        {
          "project": "project-Fkb6Gkj433GVVvj73J7x8KbV",
          "path": "/assets/mosdepth/"
        }
      ]
    }
  ],
  "outputSpec": [
    {
      "name": "mosdepth_output",
      "label": "array of mosdepth output files",
      "class": "array:file",
      "patterns": [
        "*"
      ],
      "help": ""
    }
  ],
  "runSpec": {
    "timeoutPolicy": {
      "*": {
        "hours": 1
      }
    },
    "assetDepends": [
      {
          "id": "record-Gb95XXQ4021Q7GXXzF33K6k9"
      },
      {
          "name": "samtools_asset",
          "version": "1.0.0",
          "project": "project-Fkb6Gkj433GVVvj73J7x8KbV",
          "folder": "/app_assets/samtools/samtools_v1.18/"
      }
    ],
    "interpreter": "bash",
    "release": "20.04",
    "distribution": "Ubuntu",
    "file": "src/eggd_mosdepth.sh",
    "version": "0"
  },
  "access": {
    "project": "CONTRIBUTE",
    "network": ["*"]
  },
  "developers": ["org-emee_1"],
  "authorizedUsers": ["org-emee_1"],
  "regionalOptions": {
    "aws:eu-central-1": {
      "systemRequirements": {
        "*": {
          "instanceType": "mem1_ssd1_v2_x4"
        }
      }
    }
  }
}