dxapp.json

{
  "name": "eggd_tso500",
  "title": "eggd_tso500",
  "summary": "Somatic variant calling for DNA & RNA samples using TSO500 local app",
  "dxapi": "1.0.0",
  "version":"2.0.1",
  "openSource": true,
  "inputSpec": [
    {
      "name": "TSO500_ruo",
      "label": "TSO500_ruo",
      "help": "Zip file containing of analysis asset",
      "class": "file",
      "patterns": ["*.zip"],
      "suggestions": [
        {
          "name": "TSO500 Local App v2.2 Asset Bundle",
          "value": {
            "$dnanexus_link": {
              "project": "project-Fkb6Gkj433GVVvj73J7x8KbV",
              "id": "file-Fz4X61Q44Bv44FyfJX1jJPj6"
            }
          }
        },
        {
          "project": "project-Fkb6Gkj433GVVvj73J7x8KbV",
          "path": "/assets/tso500_localApp/v2.2/"
        }
      ],
      "optional": false,
      "group": "files"
    },
    {
      "name": "run_tar_data",
      "label": "run tar data",
      "help": "tar files of runfolder containing raw sequencing data",
      "class": "array:file",
      "patterns": ["*.tar.gz"],
      "optional": false,
      "group": "files"
    },
    {
      "name": "samplesheet",
      "label": "samplesheet",
      "help": "Samplesheet to use for demultiplexing and analysis",
      "class": "file",
      "optional": true,
      "patterns": ["*.csv"],
      "group": "files"
    },
    {
      "name": "analysis_options",
      "label": "analysis_options",
      "help": "An optional string passed to analysis script",
      "class": "string",
      "optional": true,
      "group": "options"
    },
    {
      "name": "scatter_instance",
      "label": "scatter instance",
      "help": "instance type to use for scatter sub jobs (default: mem1_ssd1_v2_x36)",
      "class": "string",
      "default": "mem1_ssd1_v2_x36",
      "group": "options"
    },
    {
      "name": "isNovaSeq",
      "label": "isNovaSeq",
      "help": "(Optional) flag to specify NovaSeq data (default: true)",
      "class": "boolean",
      "default": true,
      "group": "options"
    },
    {
      "name": "upload_demultiplex_output",
      "label": "upload demultiplex output",
      "help": "(Optional) controls whether demultiplexed files are retained (true) or discarded (false)",
      "class": "boolean",
      "default": true,
      "group": "options"
    },
    {
      "name": "demultiplex_only",
      "label": "demultiplex only",
      "help": "(Optional) flag to demultiplex a runfolder and upload the fastq files",
      "class": "boolean",
      "default": false,
      "group": "options"
    },
    {
      "name": "include_samples",
      "label": "include samples",
      "help": "comma separated string of samples to run analysis on (i.e. subset of samplesheet)",
      "class": "string",
      "optional": true,
      "group": "options"
    },
    {
      "name": "exclude_samples",
      "label": "exclude samples",
      "help": "comma separated string of samples to NOT run analysis on",
      "class": "string",
      "optional": true,
      "group": "options"
    },
    {
      "name": "n_samples",
      "label": "no. samples",
      "help": "maximum number of samples from samplesheet to run analysis on (this will take the first n sample rows from the samplesheet)",
      "class": "int",
      "optional": true,
      "group": "testing"
    }
  ],
  "outputSpec": [
    {
      "name": "fastqs",
      "label": "fastqs",
      "class": "array:file",
      "help": "fastqs from demultiplexing",
      "optional": true
    },
    {
      "name": "dna_bams",
      "label": "DNA bams",
      "class": "array:file",
      "help": "stitched realigned bam files",
      "optional": true
    },
    {
      "name": "dna_bam_index",
      "label": "DNA bam index",
      "class": "array:file",
      "help": "stitched realigned bam file index",
      "optional": true
    },
    {
      "name": "rna_bams",
      "label": "RNA bams",
      "class": "array:file",
      "help": "RNA aligned bam files",
      "optional": true
    },
    {
      "name": "rna_bam_index",
      "label": "RNA bam index",
      "class": "array:file",
      "help": "RNA aligned bam file index",
      "optional": true
    },
    {
      "name": "gvcfs",
      "label": "genome VCFs",
      "class": "array:file",
      "optional": true
    },
    {
      "name": "cnv_vcfs",
      "label": "CNV VCFs",
      "class": "array:file",
      "optional": true
    },
    {
      "name": "splice_variants_vcfs",
      "label": "splice variants VCFs",
      "class": "array:file",
      "optional": true
    },
    {
      "name": "msi_metrics",
      "label": "MSI metrics",
      "class": "array:file",
      "optional": true
    },
    {
      "name": "tmb_metrics",
      "label": "TMB metrics",
      "class": "array:file",
      "optional": true
    },
    {
      "name": "small_variant_annotation",
      "label": "small variant annotation",
      "class": "array:file",
      "optional": true,
      "help": "Nirvana annotated variants in JSON format"
    },
    {
      "name": "splice_variant_annotation",
      "label": "splice variant annotation",
      "class": "array:file",
      "optional": true,
      "help": "annotated splice variants in JSON format"
    },
    {
      "name": "fusions",
      "label": "fusions",
      "class": "array:file",
      "optional": true,
      "help": "csv of identified fusions from RNA samples"
    },
    {
      "name": "cvo",
      "label": "combined variant outputs",
      "class": "array:file",
      "help": "combined variant output tsv files",
      "optional": true
    },
    {
      "name": "metricsOutput",
      "label": "MetricsOutput",
      "class": "file",
      "help": "Run level MetricsOuput.tsv file",
      "optional": true
    },
    {
      "name": "analysis_folder",
      "label": "analysis_folder",
      "help": "All other files within the analysis folder.",
      "class": "array:file",
      "optional": true
    },
    {
      "name": "demultiplex_logs",
      "label": "demultiplex logs",
      "class": "array:file",
      "optional":true,
      "help": "all intermediate and log files from demultiplexing"
    },
    {
      "name": "logs",
      "label": "logs",
      "help": "stdout logs created during analysis",
      "class": "array:file",
      "optional": true
    }
  ],
  "runSpec": {
    "execDepends": [
    ],
    "distribution" : "Ubuntu",
    "release":"20.04",
    "version":"0",
    "file": "src/code.sh",
    "interpreter": "bash",
    "headJobOnDemand": true,
    "timeoutPolicy": {
      "*": {
        "hours": 12
      }
    },
    "assetDepends": [
    ]
  },
  "developers":[
    "org-emee_1"
  ],
  "authorizedUsers": [
    "org-emee_1"
  ],
  "access": {
    "allProjects":"UPLOAD"
  },
  "regionalOptions": {
    "aws:eu-central-1": {
      "systemRequirements": {
        "main": {
          "instanceType": "mem1_ssd1_v2_x36"
        }
      }
    }
  }
}