[
    {
        "id": "snap_index",
        "name": "Scalable Nucleotide Alignment Program",
        "article": "arXiv:1111.5572v1",
        "website": "https:\/\/www.microsoft.com\/en-us\/research\/project\/snap\/",
        "git": "https:\/\/github.com\/amplab\/snap",
        "description": "fast and accurate aligner for short DNA reads. It is optimized for modern read lengths of 100 bases or higher, and align them quickly through a hash-based indexing scheme.",
        "version": "2.0.3",
        "documentation": "https:\/\/github.com\/amplab\/snap\/tree\/master\/docs",
        "multiqc": "custom",
        "commands": [
            {
                "name": "snap_index",
                "cname": "snap index",
                "command": "snap-aligner index",
                "category": "indexing",
                "output_dir": "snap\/index",
                "inputs": [
                    {
                        "name": "genome_fasta",
                        "type": "contigs",
                        "description": "Fasta reference",
                        "from": "parameter"
                    }
                ],
                "outputs": [
                    {
                        "name": "index",
                        "type": "snap_index",
                        "file": "index",
                        "description": "Index files for snap alignment"
                    }
                ],
                "options": [
                    {
                        "name": "snap_index_threads",
                        "prefix": "-t",
                        "type": "numeric",
                        "value": 4,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "Number of threads to use"
                    },
                    {
                        "name": "snap_index_genome_fasta",
                        "type": "input_file",
                        "value": "",
                        "label": "Path to reference genome fasta file"
                    },
                    {
                        "name": "snap_index_seed_size",
                        "prefix": "-s",
                        "type": "numeric",
                        "value": 24,
                        "min": 12,
                        "max": 64,
                        "step": 1,
                        "label": "seed size"
                    }
                ]
            }
        ],
        "install": [],
        "citations": {
            "snap": [
                "Faster and More Accurate Sequence Alignment with SNAP. Matei Zaharia, William J. Bolosky, Kristal Curtis, Armando Fox, David Patterson, Scott Shenker, Ion Stoica, Richard M. Karp, and Taylor Sittler. arXiv:1111.5572v1, November 2011."
            ]
        },
        "yaml": "{\n  id: snap_index,\n  name: Scalable Nucleotide Alignment Program,\n  article: \"arXiv:1111.5572v1\",\n  website: \"https:\/\/www.microsoft.com\/en-us\/research\/project\/snap\/\",\n  git: \"https:\/\/github.com\/amplab\/snap\",\n  description: \"fast and accurate aligner for short DNA reads. It is optimized for modern read lengths of 100 bases or higher, and align them quickly through a hash-based indexing scheme.\",\n  version: \"2.0.3\",\n  documentation: \"https:\/\/github.com\/amplab\/snap\/tree\/master\/docs\",\n  multiqc: \"custom\",\n  commands:\n    [\n      {\n        name: snap_index,\n        cname:  \"snap index\",\n        command: snap-aligner index,\n        category: \"indexing\",\n        output_dir: snap\/index,\n        inputs: [{ name: genome_fasta, type: \"contigs\", description: \"Fasta reference\", from: \"parameter\" }],\n        outputs: [{ name: index, type: \"snap_index\", file: index, description: \"Index files for snap alignment\" }],\n        options:\n          [\n            {\n              name: snap_index_threads,\n              prefix: -t,\n              type: numeric,\n              value: 4,\n              min: 1,\n              max: NA,\n              step: 1,\n              label: \"Number of threads to use\",\n            },\n            {\n              name: snap_index_genome_fasta,\n              type: input_file,\n              value: \"\",\n              label: \"Path to reference genome fasta file\",\n            },\n            {\n              name: snap_index_seed_size,\n              prefix: -s,\n              type: numeric,\n              value: 24,\n              min: 12,\n              max: 64,\n              step: 1,\n              label: \"seed size\",\n            }\n          ]\n      },\n    ],\n    install:  {\n    # snap: [\n    #   \"cd \/opt\/biotools\",\n    #   \"git clone https:\/\/github.com\/amplab\/snap.git\",\n    #   \"cd snap\",\n    #   \"make -j 8\",\n    #   \"ENV PATH \/opt\/biotools\/snap:$PATH\",\n    # ]\n  },\n  citations:  {\n    snap: [\n      \"Faster and More Accurate Sequence Alignment with SNAP. Matei Zaharia, William J. Bolosky, Kristal Curtis, Armando Fox, David Patterson, Scott Shenker, Ion Stoica, Richard M. Karp, and Taylor Sittler. arXiv:1111.5572v1, November 2011.\"\n    ]\n  }\n}"
    }
]