dxapp.json

{
    "name": "vcfscope-measure",
    "title": "VCFscope: Measure Genomic Pipeline Performance",
    "summary": "Calculate variant calling performance metrics from a single-sample VCF of NA12878 calls, and matched BAM file",
    "dxapi": "1.0.0",
    "version": "auto-updated-by-bamboo",
    "resources": "project-F1GG4100pVjJqZP0B1P9X9Vy",
    "contactOrgs": "http://www.garvan.org.au/kccg",
    "developers": [ "org-garvan_kccg_developers" ],
    "authorizedUsers": [ "org-garvan_kccg", "org-garvan_kccg_developers" ],
    "categories": [ "Reports", "Statistics" ],
    "inputSpec": [
        {
            "name": "vcfgz",
            "label": "Variants",
            "help": "Input NA12878 genotype calls to be validated, in vcf.gz format.",
            "class": "file",
            "patterns": [ "*.vcf.gz" ]
        },
        {
            "name": "bam",
            "label": "Mapped reads",
            "help": "The mapped NA12878 reads used to generate the genotype calls being tested, in bam format.",
            "class": "file",
            "patterns": [ "*.bam" ]
        },
        {
            "name": "bai",
            "label": "Mapped read index",
            "help": "An index for the mapped reads.",
            "class": "file",
            "patterns": [ "*.bai" ]
        },
        {
            "group": "advanced",
            "name": "region",
            "label": "Region BED",
            "help": "Limit analysis to the regions in this BED only.",
            "class": "file",
            "patterns": [ "*.bed" ],
            "optional": true
        },
        {
            "group": "advanced",
            "name": "store_variants",
            "label": "Store variants",
            "help": "Store all region-filtered variant calls in the output RDS.",
            "class": "boolean",
            "default": false
        }
    ],
    "outputSpec": [
        {
            "patterns": [
                "*.vcfscope.rds"
            ],
            "label": "VCFscope results RDS",
            "help": "An RDS (R data serialization) file containing VCFscope performance metrics.",
            "name": "rds",
            "class": "file"
        }
    ],
    "runSpec": {
        "execDepends": [
            { "name": "openjdk-7-jre-headless" }
        ],
        "systemRequirements": {
            "main": {
                "instanceType": "mem1_ssd1_x32"
            }
        },
        "assetDepends": [
            {
                "id": "record-F1JXX1j09267BZF2PF5X6pY1"
            }
        ],
        "file": "src/code.sh",
        "interpreter": "bash",
        "distribution": "Ubuntu",
        "release": "14.04"
    }
}