[
    {
        "id": "bwa_mem2_index",
        "name": "BWA MEM2 index",
        "article": "10.1109\/IPDPS.2019.00041",
        "website": "https:\/\/github.com\/bwa-mem2\/bwa-mem2",
        "git": "https:\/\/github.com\/bwa-mem2\/bwa-mem2",
        "description": "Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~80% faster (WIP; not recommended for production uses at the moment)",
        "version": "2.2.1",
        "documentation": "http:\/\/bio-bwa-mem2.sourceforge.net\/bwa-mem2.shtml",
        "multiqc": "custom",
        "commands": [
            {
                "name": "bwa_mem2_index",
                "cname": "Bwa mem 2 index",
                "command": "bwa-mem2 index",
                "category": "indexing",
                "output_dir": "bwa_mem2\/index",
                "inputs": [
                    {
                        "name": "genome_fasta",
                        "type": "contigs",
                        "description": "Fasta reference",
                        "from": "parameter"
                    }
                ],
                "outputs": [
                    {
                        "name": "index",
                        "type": "bwa_mem_2_index",
                        "file": "index",
                        "description": "Index files for bwa-mem2 alignment"
                    }
                ],
                "options": [
                    {
                        "name": "bwa_mem2_index_genome_fasta",
                        "type": "input_file",
                        "accept": [
                            ".fasta",
                            ".fa",
                            ".fasta.gz",
                            ".fa.gz"
                        ],
                        "value": "",
                        "multiple": false,
                        "label": "Path to reference genome fasta file"
                    }
                ]
            }
        ],
        "install": [],
        "citations": {
            "bwa_mem2": [
                "Vasimuddin Md, Sanchit Misra, Heng Li, Srinivas Aluru. Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. IEEE Parallel and Distributed Processing Symposium (IPDPS), 2019"
            ]
        },
        "yaml": "{\n  id: bwa_mem2_index,\n  name: BWA MEM2 index,\n  article: 10.1109\/IPDPS.2019.00041,\n  website: \"https:\/\/github.com\/bwa-mem2\/bwa-mem2\",\n  git: \"https:\/\/github.com\/bwa-mem2\/bwa-mem2\",\n  description: \"Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~80% faster (WIP; not recommended for production uses at the moment)\",\n  version: \"2.2.1\",\n  documentation: \"http:\/\/bio-bwa-mem2.sourceforge.net\/bwa-mem2.shtml\",\n  multiqc: \"custom\",\n  commands:\n    [\n      {\n        name: bwa_mem2_index,\n        cname: \"Bwa mem 2 index\",\n        command: bwa-mem2 index,\n        category: \"indexing\",\n        output_dir: bwa_mem2\/index,\n        inputs: [{ name: genome_fasta, type: \"contigs\", description: \"Fasta reference\", from: \"parameter\" }],\n        outputs: [{ name: index, type: \"bwa_mem_2_index\", file: index, description: \"Index files for bwa-mem2 alignment\" }],\n        options:\n          [\n            {\n              name: bwa_mem2_index_genome_fasta,\n              type: input_file,\n              accept: [\".fasta\",\".fa\",\".fasta.gz\",\".fa.gz\"],\n              value: \"\",\n              multiple: FALSE,\n              label: \"Path to reference genome fasta file\",\n            }\n          ]\n      },\n    ],\n  install:  {\n    # bwa_mem2: [\n    #   \"cd \/opt\/biotools\",\n    #   \"wget https:\/\/github.com\/bwa-mem2\/bwa-mem2\/releases\/download\/v2.2.1\/bwa-mem2-2.2.1_x64-linux.tar.bz2\",\n    #   \"tar -xvjf bwa-mem2-2.2.1_x64-linux.tar.bz2\",\n    #   \"mv bwa-mem2-2.2.1_x64-linux\/bwa-mem2* \/opt\/biotools\/bin\/\",\n    #   \"rm -r bwa-mem2-2.2.1_x64-linux bwa-mem2-2.2.1_x64-linux.tar.bz2\"\n    # ],\n  },\n  citations:  {\n    bwa_mem2: [\n      \"Vasimuddin Md, Sanchit Misra, Heng Li, Srinivas Aluru. Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. IEEE Parallel and Distributed Processing Symposium (IPDPS), 2019\"\n    ]\n  }\n}"
    }
]