[
    {
        "id": "bowtie2_index",
        "name": "Bowtie2 index",
        "article": "10.1038\/nmeth.1923",
        "website": "http:\/\/bowtie-bio.sourceforge.net\/bowtie2\/index.shtml",
        "git": "https:\/\/github.com\/BenLangmead\/bowtie2",
        "description": "A fast and sensitive gapped read aligner",
        "version": "2.5.1",
        "documentation": "http:\/\/bowtie-bio.sourceforge.net\/bowtie2\/manual.shtml",
        "multiqc": "bowtie2",
        "commands": [
            {
                "name": "bowtie2_index",
                "cname": "Bowtie2 index",
                "command": "bowtie2-build",
                "category": "indexing",
                "output_dir": "bowtie2\/index",
                "inputs": [
                    {
                        "name": "genome_fasta",
                        "type": "contigs",
                        "description": "Fasta reference"
                    }
                ],
                "outputs": [
                    {
                        "name": "index",
                        "type": "bowtie2_index",
                        "file": "index",
                        "description": "Index files for bowtie2 alignment"
                    }
                ],
                "options": [
                    {
                        "name": "bowtie2_index_threads",
                        "prefix": "--threads",
                        "type": "numeric",
                        "value": 4,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "Number of threads to use to index genome"
                    }
                ]
            }
        ],
        "install": [],
        "citations": {
            "bowtie2": [
                "Langmead, B., Salzberg, S. Fast gapped-read alignment with Bowtie 2. Nat Methods 9, 357-359 (2012). https:\/\/doi.org\/10.1038\/nmeth.1923"
            ]
        },
        "yaml": "{\n  id: bowtie2_index,\n  name: Bowtie2 index,\n  article: 10.1038\/nmeth.1923,\n  website: \"http:\/\/bowtie-bio.sourceforge.net\/bowtie2\/index.shtml\",\n  git: \"https:\/\/github.com\/BenLangmead\/bowtie2\",\n  description: \"A fast and sensitive gapped read aligner\",\n  version: \"2.5.1\",\n  documentation: \"http:\/\/bowtie-bio.sourceforge.net\/bowtie2\/manual.shtml\",\n  multiqc: \"bowtie2\",\n  commands:\n    [\n      {\n        name: bowtie2_index,\n        cname:  \"Bowtie2 index\",\n        command: bowtie2-build,\n        category: \"indexing\",\n        output_dir: bowtie2\/index,\n        inputs: [{ name: genome_fasta, type: \"contigs\", description: \"Fasta reference\"}], #, from: \"parameter\" }],\n        outputs: [{ name: index, type: \"bowtie2_index\", file: index, description: \"Index files for bowtie2 alignment\" }],\n        options:\n          [\n            {\n              name: bowtie2_index_threads,\n              prefix: --threads,\n              type: numeric,\n              value: 4,\n              min: 1,\n              max: NA,\n              step: 1,\n              label: \"Number of threads to use to index genome\",\n            }\n          ]\n      },\n    ],\n  install:  {\n    # bowtie2: [\n    #   \"wget -O bowtie2-2.4.1-linux-x86_64.zip https:\/\/github.com\/BenLangmead\/bowtie2\/releases\/download\/v2.4.1\/bowtie2-2.4.1-linux-x86_64.zip\",\n    #   \"unzip bowtie2-2.4.1-linux-x86_64.zip\",\n    #   \"cp bowtie2-2.4.1-linux-x86_64\/bowtie2* \/usr\/bin\",\n    #   \"rm -rf bowtie2-2.4.1*\"\n    # ],\n  },\n  citations:  {\n    bowtie2: [\n      \"Langmead, B., Salzberg, S. Fast gapped-read alignment with Bowtie 2. Nat Methods 9, 357-359 (2012). https:\/\/doi.org\/10.1038\/nmeth.1923\"\n    ],\n  }\n}"
    }
]