bwa_mem.json

{
    "name": "rb-BWA-mem",
    "parallelism": "SERIAL",
    "version": "0.7.12",
    "revision": 1,
    "helpURI": "http://bioinformatics-centre.github.io/bayesembler/",
    "label": "BWA-mem",
    "shortDescription": "BWA-mem mapper",
    "longDescription": "Maps reads including longer reads to a reference sequence.",
    "author": "Roger Barthelson",
    "datePublished": "10/18/15",
    "tags": [
        "aligner",
        "NGS",
        "Illumina"
    ],
    "ontology": [
        "http://sswapmeet.sswap.info/sequenceServices/SequenceServices"
    ],
    "defaultMaxRunTime": "35:56:00",
    "defaultQueue": "normal",
    "defaultNodeCount": 1,
    "defaultMemoryPerNode": 32,
    "defaultProcessorsPerNode": 16,
    "executionHost": "rogerab-stampedesville",
    "executionSystem": "rogerab-stampedesville",
    "executionType": "HPC",
    "deploymentPath": "rogerab/applications/bwa-mem/bin",
    "templatePath": "bwa_wrapper.sh",
    "testPath": "../test/bwa_wrapper_test.sh",
    "checkpointable": true,
    "modules": [
        "purge",
        "load TACC",
        "load irods",
        "load bwa/0.7.12",
	"load samtools/1.2"
    ],
    "inputs": [
        {
            "id": "seqFolder",
            "value": {
                "default": "",
                "validator": "",
                "visible": true,
                "required": false,
                "order": 1
            },
            "details": {
                "label": "Directory of NGS files",
                "description": "Reads input directory"
            },
            "semantics": {
                "ontology": [
                    "http://sswapmeet.sswap.info/sequence/FASTA"
                ],
                "minCardinality": 1,
                "fileTypes": [
                    "directory"
                ]
            }
        },
              {
            "id": "reference",
            "value": {
                "default": "",
                "validator": "",
                "visible": true,
                "required": false,
                "order": 2
            },
            "details": {
                "label": "reference fasta",
                "description": "reference genome file."
            },
            "semantics": {
                "ontology": [
                    "http://sswapmeet.sswap.info/sequence/FASTA"
                ],
                "minCardinality": 1,
                "fileTypes": [
                    "fasta-0"
                ]
            }
        },
              {
            "id": "reference_data",
            "value": {
                "default": "",
                "validator": "",
                "visible": true,
                "required": false,
                "order": 3
            },
            "details": {
                "label": "indexed reference",
                "description": "pre-indexed reference sequence -- tarred and zipped."
            },
            "semantics": {
                "ontology": [
                    "http://sswapmeet.sswap.info/sequence/FASTA"
                ],
                "minCardinality": 1,
                "fileTypes": [
                    "fasta-0"
                ]
            }
        }
                ],
    "parameters": [
                    {
            "id": "seqmode",
            "value": {
                "default": "paired",
                "type": "enumeration",
                "enum_values": [
                    { "paired": "paired"},
                    { "unpaired": "unpaired"}
                ],
                "required": true,
                "visible": true,
                "order": 1
            },
            "details": {
                "label": "paired vs unpaired reads",
                "description": "Sequencing mode, paired vs unpaired",
                "visible": true
            },
            "semantics": {
                "ontology": [
                    "xs:string"
                ]
            }
        },
        {
            "id": "min_score",
            "value": {
                "default": "",
                "validator": "",
                "required": false,
                "visible": true,
                "type": "string"
            },
            "details": {
                "label": "minimum score",
                "description": "Minimum score to output",
                "visible": true,
                "order": 2
            },
            "semantics": {
                "ontology": [
                    "xs:string"
                ]
            }
        },        
                    {
            "id": "read_type",
            "value": {
                "default": "",
                "type": "enumeration",
                "enum_values": [
                    { "": "Illumina, default"},
                    { "pacbio": "PacBio"},
                    { "ont2d": "Oxford Nanopore"},
                    { "intractg": "Intra-species contigs to ref"}
                ],
                "required": false,
                "visible": true,
                "order": 3
            },
            "details": {
                "label": "read type",
                "description": "type of sequencing reads",
                "visible": true
            },
            "semantics": {
                "ontology": [
                    "xs:string"
                ]
            }
        },
                    {
            "id": "sort_type",
            "value": {
                "default": "",
                "type": "enumeration",
                "enum_values": [
                    { "": "by coordinates"},
                    { "-n": "by name"}
                ],
                "required": false,
                "visible": true,
                "order": 3
            },
            "details": {
                "label": "Sorting method for the BAM file",
                "description": "coordinate sorting or name sorting",
                "visible": true
            },
            "semantics": {
                "ontology": [
                    "xs:string"
                ]
            }
        }
    ],
    "outputs": [
        {
            "id": "bwa_output",
            "details": {
                "label": "Output Directory",
                "description": "The output directory."
            },
            "semantics": {
                "ontology": [],
                "minCardinality": 1,
                "maxCardinality": 1,
                "fileTypes": [
                    "TEXT-0"
                ]
            },
            "value": {
                "default": "BWA_output",
                "required": true,
                "type": "string",
                "visible": false
            }
        }
    ]
}