dxapp.json

{
  "name": "udn_star2.6.0c",
  "title": "udn_star2.6.0c",
  "summary": "udn_star2.6.0c",
  "dxapi": "1.0.0",
  "version": "0.0.1",
  "inputSpec": [
    {
      "name": "read1_fastq",
      "label": "read1_fastq",
      "class": "file",
      "optional": false,
      "patterns": [
        "*.gz"
      ],
      "help": "gzip file of read1 fastq"
    },
    {
      "name": "read2_fastq",
      "label": "read2_fastq",
      "class": "file",
      "optional": false,
      "patterns": [
        "*.gz"
      ],
      "help": "gzip file of read2 fastq"
    },
    {
      "name": "star_index_75bp",
      "label": "star_index_75bp",
      "class": "file",
      "optional": false,
      "patterns": [
        "*.tar"
      ],
      "help": "STAR index file for 75bp reads (tar format, no need to compress)"
    },
    {
      "name": "star_index_69bp",
      "label": "star_index_69bp",
      "class": "file",
      "optional": true,
      "patterns": [
        "*.tar"
      ],
      "help": "STAR index for 69bp reads"
    },
    {
      "name": "star_index_120bp",
      "label": "star_index_120bp",
      "class": "file",
      "optional": true,
      "patterns": [
        "*.tar"
      ],
      "help": "STAR index for 120bp reads"
    },    
    {
      "name": "sample",
      "label": "sample",
      "class": "string",
      "optional": false,
      "help": "Sample ID for SAM header"
    },
    {
      "name": "library",
      "label": "library",
      "class": "string",
      "optional": true,
      "help": "Optional: Library for SAM header (otherwise will be automatically set to sample name)"
    }
  ],
  "outputSpec": [
    {
      "name": "aligned_bam",
      "label": "aligned_bam",
      "class": "file",
      "patterns": [
        "*.Aligned.out.bam"
      ],
      "help": "STAR genome alignment (Unsorted!)"
    },
    {
      "name": "transcriptome_bam",
      "label": "transcriptome_bam",
      "class": "file",
      "patterns": [
        "*.Aligned.toTranscriptome.out.bam"
      ],
      "help": "STAR transcriptome alignment"
    },
    {
      "name": "sjout_tab",
      "label": "sjout_tab",
      "class": "file",
      "patterns": [
        "*.SJ.out.tab.gz"
      ],
      "help": "STAR splice junction table"
    },
    {
      "name": "final_log",
      "label": "final_log",
      "class": "file",
      "patterns": [
        "*.Log.final.out"
      ],
      "help": "STAR final log file"
    }
  ],
  "runSpec": {
    "timeoutPolicy": {
      "*": {
        "hours": 10
      }
    },
    "interpreter": "bash",
    "release": "14.04",
    "distribution": "Ubuntu",
    "file": "src/udn_star2.6.0c.sh"
  },
  "regionalOptions": {
    "aws:us-east-1": {
      "systemRequirements": {
        "*": {
          "instanceType": "mem2_ssd1_x8"
        }
      }
    }
  }
}