[
    {
        "id": "bowtie_index",
        "name": "Bowtie index",
        "article": "10.1002\/0471250953.bi1107s32",
        "website": "http:\/\/bowtie-bio.sourceforge.net",
        "git": "https:\/\/github.com\/BenLangmead\/bowtie",
        "description": "Bowtie is an ultrafast, memory-efficient short read aligner.",
        "version": "1.3.1",
        "documentation": "http:\/\/bowtie-bio.sourceforge.net\/manual.shtml",
        "multiqc": "bowtie1",
        "commands": [
            {
                "name": "bowtie_index",
                "cname": "Bowtie index",
                "command": "bowtie-build",
                "category": "indexing",
                "output_dir": "bowtie\/index",
                "inputs": [
                    {
                        "name": "genome_fasta",
                        "type": "contigs",
                        "description": "Fasta reference"
                    }
                ],
                "outputs": [
                    {
                        "name": "index",
                        "type": "bowtie_index",
                        "file": "index",
                        "description": "Index files for bowtie alignment"
                    }
                ],
                "options": [
                    {
                        "name": "bowtie_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": {
            "bowtie": [
                "Langmead, B., Trapnell, C., Pop, M. et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25 (2009). https:\/\/doi.org\/10.1186\/gb-2009-10-3-r25"
            ]
        },
        "yaml": "{\n  id: bowtie_index,\n  name: Bowtie index,\n  article: 10.1002\/0471250953.bi1107s32,\n  website: \"http:\/\/bowtie-bio.sourceforge.net\",\n  git: \"https:\/\/github.com\/BenLangmead\/bowtie\",\n  description: \"Bowtie is an ultrafast, memory-efficient short read aligner.\",\n  version: \"1.3.1\",\n  documentation: \"http:\/\/bowtie-bio.sourceforge.net\/manual.shtml\",\n  multiqc: \"bowtie1\",\n  commands:\n    [\n      {\n        name: bowtie_index,\n        cname:  \"Bowtie index\",\n        command: bowtie-build,\n        category: \"indexing\",\n        output_dir: bowtie\/index,\n        inputs: [{ name: genome_fasta, type: \"contigs\", description: \"Fasta reference\"}], # from: \"parameter\" }],\n        outputs: [{ name: index, type: \"bowtie_index\", file: index, description: \"Index files for bowtie alignment\" }],\n        options:\n          [\n            {\n              name: bowtie_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    # bowtie: [\n    #   \"wget -O bowtie-1.3.0-linux-x86_64.zip https:\/\/sourceforge.net\/projects\/bowtie-bio\/files\/bowtie\/1.3.0\/bowtie-1.3.0-linux-x86_64.zip\/download\",\n    #   \"unzip bowtie-1.3.0-linux-x86_64.zip\",\n    #   \"cp bowtie-1.3.0-linux-x86_64\/bowtie* \/usr\/bin\",\n    #   \"rm -rf bowtie-1.3.0*\"\n    # ],\n  },\n  citations:  {\n    bowtie: [\n      \"Langmead, B., Trapnell, C., Pop, M. et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25 (2009). https:\/\/doi.org\/10.1186\/gb-2009-10-3-r25\"\n    ],\n  }\n}"
    }
]