dxapp.json

{
  "name": "eggd_bcl2fastq2.20",
  "title": "BCL to FASTQ v2.20",
  "version": "1.2.1",
  "summary": "Converts Illumina data from BCL to FASTQ using bcl2fastq v2.20 demultiplexing barcoded samples, for use with NextSeq, HiSeq, NovaSeq",
  "tags": ["Read Mapping"],
  "dxapi": "1.0.0",
  "inputSpec": [
    {
      "name": "upload_sentinel_record",
      "label": "Incremental upload sentinel record",
      "help": "The sentinel record produced by the the incremental_upload.sh script. When this record is closed it indicates that the upload is complete and bcl2fastq can begin.",
      "class": "record",
      "optional": true
    },
    {
      "name": "run_archive",
      "label": "Archive of top level run folder",
      "help": "One archived file containing the top level output from the run. This archive should contain RunInfo.xml and be named the same as the original file.",
      "class": "array:file",
      "patterns": ["*.rar", "*.zip", "*.tar.gz", "*.tgz"],
      "optional": true
    },
    {
      "name": "sample_sheet",
      "label": "Sample sheet",
      "help": "The sample sheet file in CSV format.",
      "class": "file",
      "patterns": ["*.csv"],
      "optional": true
    },
    {
      "name": "advanced_opts",
      "label": "Advanced options",
      "help": "Additional command-line options to be passed verbatim to the invocation of bcl2fastq.",
      "class": "string",
      "optional": true,
      "default": "-l INFO",
      "group": "Advanced"
    }
  ],
  "outputSpec": [
    {
      "name": "output",
      "label": "All files (except bcls) from the sequencer after demultiplexing",
      "help": "An array of files with run statistics",
      "class": "array:file"
    }
  ],
  "runSpec": {
    "file": "src/code.sh",
    "release": "20.04",
    "version": "0",
    "interpreter": "bash",
    "distribution": "Ubuntu",
    "assetDepends": [
      {
        "name": "bcl2fastq",
        "version": "2.20",
        "project": "project-Fkb6Gkj433GVVvj73J7x8KbV",
        "folder": "/assets/bcl2fastq"
      }
    ]
  },
  "access": {
    "project": "UPLOAD",
    "allProjects":"UPLOAD"
  },
  "developers":[
    "org-emee_1"
  ],
  "authorizedUsers": [
    "org-emee_1"
  ],
  "details": {
    "upstreamAuthor": "Illumina",
    "upstreamVersion": "2.20",
    "upstreamLicenses": ["-"],
    "citations": ["-"],
    "whatsNew": "* 0.0.1: New app for converting bcl to fastq with bcl2fastq2.20",
    "upstreamUrl": "https://support.illumina.com/content/dam/illumina-support/documents/documentation/software_documentation/bcl2fastq/bcl2fastq2_guide_15051736_v2.pdf"
  },
  "ignoreReuse": false,
  "regionalOptions": {
    "aws:eu-central-1": {
      "systemRequirements": {
        "*": {
          "instanceType": "mem2_ssd1_v2_x32"
        }
      }
    }
  }
}