[
    {
        "id": "hisat2_index",
        "name": "hisat2 index",
        "article": "Kim, D., Paggi, J.M., Park, C. et al. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol 37, 907-915 (2019).",
        "website": "http:\/\/daehwankimlab.github.io\/hisat2\/",
        "git": "http:\/\/daehwankimlab.github.io\/hisat2\/",
        "description": "a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA)",
        "version": "2.2.1",
        "documentation": "http:\/\/daehwankimlab.github.io\/hisat2\/manual\/",
        "multiqc": "hisat2",
        "commands": [
            {
                "name": "hisat2_index",
                "cname": "hisat2 index",
                "command": "hisat2-build",
                "category": "indexing",
                "output_dir": "hisat2\/index",
                "inputs": [
                    {
                        "name": "genome_fasta",
                        "type": "contigs",
                        "description": "Fasta reference",
                        "from": "parameter"
                    }
                ],
                "outputs": [
                    {
                        "name": "index",
                        "type": "hisat2_index",
                        "file": "index",
                        "description": "Index files for hisat2 alignment"
                    }
                ],
                "options": [
                    {
                        "name": "hisat2_index_genome_fasta",
                        "type": "input_file",
                        "value": "",
                        "label": "Path to reference genome fasta file"
                    },
                    {
                        "name": "hisat2_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": {
            "hisat2": [
                "Kim, D., Paggi, J.M., Park, C. et al. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol 37, 907-915 (2019)"
            ]
        },
        "yaml": "{\n  id: hisat2_index,\n  name: hisat2 index,\n  article: \"Kim, D., Paggi, J.M., Park, C. et al. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol 37, 907-915 (2019).\",\n  website: \"http:\/\/daehwankimlab.github.io\/hisat2\/\",\n  git: \"http:\/\/daehwankimlab.github.io\/hisat2\/\",\n  description: \"a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA)\",\n  version: \"2.2.1\",\n  documentation: \"http:\/\/daehwankimlab.github.io\/hisat2\/manual\/\",\n  multiqc: \"hisat2\",\n  commands:\n    [\n      {\n        name: hisat2_index,\n        cname:  \"hisat2 index\",\n        command: hisat2-build,\n        category: \"indexing\",\n        output_dir: hisat2\/index,\n        inputs: [{ name: genome_fasta, type: \"contigs\", description: \"Fasta reference\", from: \"parameter\" }],\n        outputs: [{ name: index, type: \"hisat2_index\", file: index, description: \"Index files for hisat2 alignment\" }],\n        options:\n          [\n            {\n              name: hisat2_index_genome_fasta,\n              type: input_file,\n              value: \"\",\n              label: \"Path to reference genome fasta file\",\n            },\n            {\n              name: hisat2_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    #  hisat2: [\n    #   \"cd \/tmp\",\n    #   \"wget -O hisat2-2.2.1-linux-x86_64.zip https:\/\/cloud.biohpc.swmed.edu\/index.php\/s\/oTtGWbWjaxsQ2Ho\/download\",\n    #   \"unzip hisat2-2.2.1-linux-x86_64.zip\",\n    #   \"mv  hisat2-2.2.1 \/opt\/biotools\/\",\n    #   \"rm -rf hisat2-2.2.1*\",\n    #   \"ENV PATH \/opt\/biotools\/hisat2-2.2.1:$PATH \",\n    #   \"echo \\\"export PATH=$PATH:\/opt\/biotools\/hisat2-2.2.1\\\" >> \/etc\/environment\"\n    # ],\n  },\n  citations:  {\n    hisat2: [\n      \"Kim, D., Paggi, J.M., Park, C. et al. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol 37, 907-915 (2019)\"\n    ],\n  }\n}"
    }
]