dxapp.json

{
  "name": "stjude_htseq_count",
  "title": "HTSeq count (St. Jude)",
  "summary": "HTSeq",
  "dxapi": "1.0.0",
  "version": "1.0.1",
  "developers": [
    "user-andrew.frantz_stjude.org",
    "user-athrashe"
  ],
  "authorizedUsers": [
    "org-stjude_cloud_app_runners",
    "org-stjude_cloud"
  ],
  "inputSpec": [
    {
      "name": "bam_file",
      "label": "bam_file",
      "class": "file",
      "patterns": [
        "*.bam"
      ],
      "optional": false
    },
    {
      "name": "gene_model",
      "label": "gene_model",
      "class": "file",
      "patterns": [
        "*.gtf",
        "*.gtf.gz",
        "*.gtf.bz2"
      ],
      "optional": false
    },
    {
      "name": "order",
      "label": "Read ordering",
      "class": "string",
      "choices": [
        "name",
        "pos"
      ],
      "default": "name"
    },
    {
      "name": "strand",
      "label": "Read strandedness",
      "class": "string",
      "choices": [
        "yes",
        "no",
        "reverse"
      ],
      "default": "yes"
    },
    {
      "name": "feature_type",
      "label": "Feature type to use from GTF file",
      "class": "string",
      "choices": [
        "exon",
        "gene",
        "transcript",
        "CDS",
        "start_codon",
        "stop_codon",
        "UTR",
        "Selenocysteine"
      ],
      "default": "exon"
    },
    {
      "name": "id_attribute",
      "label": "GTF attribute to use as ID",
      "class": "string",
      "choices": [
        "gene_id",
        "gene_name",
        "transcript_id",
        "transcript_name"
      ],
      "default": "gene_name"
    },
    {
      "name": "additional_attr",
      "label": "Additional feature attributes",
      "class": "string",
      "optional": true,
      "choices": [
        "gene_id",
        "gene_name",
        "transcript_id",
        "transcript_name"
      ]
    },
    {
      "name": "mode",
      "label": "Mode to handle overlapping reads",
      "class": "string",
      "choices": [
        "union",
        "intersection-strict",
        "intersection-empty"
      ],
      "default": "union"
    },
    {
      "name": "nonunique",
      "label": "Mode for non-unique reads",
      "class": "string",
      "choices": [
        "none",
        "all"
      ],
      "default": "none"
    },
    {
      "name": "secondary_alignments",
      "label": "Mode for secondary alignments",
      "class": "string",
      "choices": [
        "score",
        "ignore"
      ],
      "default": "score"
    },
    {
      "name": "supplementary_alignments",
      "label": "Mode for supplementary alignments",
      "class": "string",
      "choices": [
        "score",
        "ignore"
      ],
      "default": "score"
    },
    {
      "name": "annotate_bam",
      "label": "Whether to output an annotated BAM",
      "class": "boolean",
      "default": false
    },
    {
      "name": "minqual",
      "label": "Minimum MAPQ alignment quality",
      "class": "int",
      "default": 10
    }
  ],
  "outputSpec": [
    {
      "name": "htseq_counts",
      "label": "HTSeq Counts",
      "class": "file"
    },
    {
      "name": "annotated_bam",
      "label": "Counts annotated BAM",
      "class": "file",
      "optional": true
    }
  ],
  "runSpec": {
    "execDepends": [
      {
        "name": "liblzma-dev"
      },
      {
        "name": "build-essential"
      }
    ],
    "systemRequirements": {
      "*": {
        "instanceType": "azure:mem2_ssd1_x8"
      }
    },
    "file": "src/code.sh",
    "release": "20.04",
    "interpreter": "bash",
    "distribution": "Ubuntu",
    "version": "0"
  },
  "access": {
    "network": [
      "*"
    ]
  }
}