[
    {
        "id": "bwa_mem_index",
        "name": "BWA MEM index",
        "article": "10.1093\/bioinformatics\/btp324",
        "website": "http:\/\/bio-bwa.sourceforge.net\/",
        "git": "https:\/\/github.com\/lh3\/bwa",
        "description": "BWA is a software package for mapping low-divergent sequences against a large reference genome.",
        "version": "0.7.17",
        "documentation": "http:\/\/bio-bwa.sourceforge.net\/bwa.shtml",
        "multiqc": "custom",
        "commands": [
            {
                "name": "bwa_mem_index",
                "cname": "Bwa mem index",
                "command": "bwa index",
                "category": "indexing",
                "output_dir": "bwa_mem_index",
                "inputs": [
                    {
                        "name": "genome_fasta",
                        "type": "contigs",
                        "description": "Fasta reference"
                    }
                ],
                "outputs": [
                    {
                        "name": "index",
                        "type": "bwa_mem_index",
                        "file": "index",
                        "description": "Index files for bwa alignment"
                    }
                ],
                "options": [
                    {
                        "name": "bwa_mem_index_algorithm",
                        "type": "radio",
                        "value": "bwtsw",
                        "choices": [
                            {
                                "bwtsw": "bwtsw"
                            },
                            {
                                "is": "is"
                            }
                        ],
                        "label": "Algorithm for constructing BWT index (see documentation for details)"
                    }
                ],
                "shell": [
                    "bwa index ",
                    "-p {params.output_prefix} ",
                    "-a {params.algorithm} ",
                    "{input} |& tee {log}"
                ]
            }
        ],
        "install": [],
        "citations": {
            "bwa": [
                "Heng Li, Richard Durbin, Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, Volume 25, Issue 14, 15 July 2009, Pages 1754-1760, https:\/\/doi.org\/10.1093\/bioinformatics\/btp324"
            ]
        },
        "yaml": "{\n  id: bwa_mem_index,\n  name: BWA MEM index,\n  article: 10.1093\/bioinformatics\/btp324,\n  website: \"http:\/\/bio-bwa.sourceforge.net\/\",\n  git: \"https:\/\/github.com\/lh3\/bwa\",\n  description: \"BWA is a software package for mapping low-divergent sequences against a large reference genome.\",\n  version: \"0.7.17\",\n  documentation: \"http:\/\/bio-bwa.sourceforge.net\/bwa.shtml\",\n  multiqc: \"custom\",\n  commands:\n    [\n      {\n        name: bwa_mem_index,\n        cname: \"Bwa mem index\",\n        command: bwa index,\n        category: \"indexing\",\n        output_dir: bwa_mem_index,\n        inputs: [{ name: genome_fasta, type: \"contigs\", description: \"Fasta reference\"}], # from: \"parameter\" }],\n        outputs: [{ name: index, type: \"bwa_mem_index\", file: index, description: \"Index files for bwa alignment\" }],\n        options:\n          [\n            {\n              name: \"bwa_mem_index_algorithm\",\n              type: \"radio\",\n              value: \"bwtsw\",\n              choices: [bwtsw: bwtsw, is: is],\n              label: \"Algorithm for constructing BWT index (see documentation for details)\",\n            }\n          ],\n        shell: [\n          \"bwa index \",\n          \"-p {params.output_prefix} \",\n          \"-a {params.algorithm} \",\n          \"{input} |& tee {log}\"\n        ]\n      },\n    ],\n  install:  {\n    # bwa: [\n    #   \"cd \/opt\/biotools\",\n    #   \"wget https:\/\/github.com\/lh3\/bwa\/releases\/download\/v0.7.17\/bwa-0.7.17.tar.bz2\",\n    #   \"tar -xvjf bwa-0.7.17.tar.bz2\",\n    #   \"cd bwa-0.7.17\",\n    #   \"make -j 10\",\n    #   \"mv bwa ..\/bin\/\",\n    #   \"cd ..\",\n    #   \"rm -r bwa-0.7.17 bwa-0.7.17.tar.bz2\"\n    # ],\n  },\n  citations:  {\n    bwa: [\n      \"Heng Li, Richard Durbin, Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, Volume 25, Issue 14, 15 July 2009, Pages 1754-1760, https:\/\/doi.org\/10.1093\/bioinformatics\/btp324\"\n    ],\n  }\n}"
    }
]