[
    {
        "id": "trinity",
        "name": "Trinity",
        "article": "10.1038\/nbt.1883",
        "website": "https:\/\/github.com\/trinityrnaseq\/trinityrnaseq\/wiki",
        "git": "https:\/\/github.com\/trinityrnaseq\/trinityrnaseq",
        "description": "Trinity assembles transcript sequences from Illumina RNA-Seq data.",
        "version": "2.15.1",
        "documentation": "https:\/\/github.com\/trinityrnaseq\/trinityrnaseq\/wiki",
        "multiqc": "custom",
        "commands": [
            {
                "name": "trinity_PE",
                "cname": "Trinity PE",
                "command": "Trinity",
                "category": "assembly",
                "output_dir": "trinity_PE",
                "inputs": [
                    {
                        "name": "read",
                        "type": "reads"
                    },
                    {
                        "name": "read2",
                        "type": "reads"
                    }
                ],
                "outputs": [
                    {
                        "name": "assembly",
                        "file": "trinity_PE.Trinity.fasta",
                        "type": "contigs",
                        "description": "assembly sequences"
                    }
                ],
                "options": [
                    {
                        "name": "trinity_threads",
                        "prefix": "--CPU",
                        "type": "numeric",
                        "value": 4,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "Number of threads to use"
                    },
                    {
                        "name": "trinity_max_memory",
                        "prefix": "--max_memory",
                        "type": "numeric",
                        "value": 10,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "Maximum memory to use by Trinity (in Giga)"
                    }
                ]
            },
            {
                "name": "trinity_SE",
                "cname": "Trinity SE",
                "command": "Trinity",
                "category": "assembly",
                "output_dir": "trinity_SE",
                "inputs": [
                    {
                        "name": "read",
                        "type": "reads"
                    }
                ],
                "outputs": [
                    {
                        "name": "assembly",
                        "file": "trinity_SE.Trinity.fasta",
                        "type": "contigs",
                        "description": "assembly sequences"
                    }
                ],
                "options": [
                    {
                        "name": "trinity_threads",
                        "prefix": "--CPU",
                        "type": "numeric",
                        "value": 4,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "Number of threads to use"
                    },
                    {
                        "name": "trinity_max_memory",
                        "prefix": "--max_memory",
                        "type": "numeric",
                        "value": 10,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "Maximum memory to use by Trinity (in Giga)"
                    }
                ]
            }
        ],
        "install": [],
        "citations": {
            "trinity": [
                "Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A. Full-length transcriptome assembly from RNA-seq data without a reference genome. Nat Biotechnol. 2011 May 15;29(7):644-52. doi: 10.1038\/nbt.1883. PubMed PMID: 21572440."
            ]
        },
        "yaml": "{\n  id: trinity,\n  name: Trinity,\n  article: \"10.1038\/nbt.1883\",\n  website: \"https:\/\/github.com\/trinityrnaseq\/trinityrnaseq\/wiki\",\n  git: \"https:\/\/github.com\/trinityrnaseq\/trinityrnaseq\",\n  description: \"Trinity assembles transcript sequences from Illumina RNA-Seq data.\",\n  version: \"2.15.1\",\n  documentation: \"https:\/\/github.com\/trinityrnaseq\/trinityrnaseq\/wiki\",\n  multiqc: \"custom\",\n  commands:\n    [\n      {\n        name: trinity_PE,\n        cname: \"Trinity PE\",\n        command: \"Trinity\" ,\n        category: \"assembly\",\n        output_dir: trinity_PE,\n        inputs: [{name: \"read\", type: \"reads\"}, {name: \"read2\", type: \"reads\"}],\n        outputs:  [{ name: \"assembly\", file: \"trinity_PE.Trinity.fasta\",type: \"contigs\", description: \"assembly sequences\" }],\n        options:\n          [\n            {\n              name: trinity_threads,\n              prefix: --CPU,\n              type: numeric,\n              value: 4,\n              min: 1,\n              max: NA,\n              step: 1,\n              label: \"Number of threads to use\",\n            },\n            {\n              name: trinity_max_memory,\n              prefix: --max_memory,\n              type: numeric,\n              value: 10,\n              min: 1,\n              max: NA,\n              step: 1,\n              label: \"Maximum memory to use by Trinity (in Giga)\",\n            },\n          ],\n      },\n      {\n        name: trinity_SE,\n        cname: \"Trinity SE\",\n        command: \"Trinity\" ,\n        category: \"assembly\",\n        output_dir: trinity_SE,\n        inputs: [{name: \"read\", type: \"reads\"}],\n        outputs:  [{ name: \"assembly\", file: \"trinity_SE.Trinity.fasta\", type: \"contigs\", description: \"assembly sequences\" }],\n        options:\n          [\n            {\n              name: trinity_threads,\n              prefix: --CPU,\n              type: numeric,\n              value: 4,\n              min: 1,\n              max: NA,\n              step: 1,\n              label: \"Number of threads to use\",\n            },\n            {\n              name: trinity_max_memory,\n              prefix: --max_memory,\n              type: numeric,\n              value: 10,\n              min: 1,\n              max: NA,\n              step: 1,\n              label: \"Maximum memory to use by Trinity (in Giga)\",\n            },\n          ],\n      },\n    ],\n  install: {\n    # trinity: [\n      # \"cd \/opt\/biotools\",\n      # \"wget https:\/\/github.com\/trinityrnaseq\/trinityrnaseq\/archive\/Trinity-v2.8.4.tar.gz\",\n      # \"tar -xvzf trinityrnaseq-Trinity-v2.8.4.tar.gz\",\n      # \"cd bin\",\n      # \"ln -s \/opt\/biotools\/trinityrnaseq-Trinity-v2.8.4\/Trinity Trinity\",\n      # \"rm trinityrnaseq-Trinity-v2.8.4.tar.gz\"\n    # ]\n  },\n  citations:\n    {\n      trinity: [\n        \"Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A. Full-length transcriptome assembly from RNA-seq data without a reference genome. Nat Biotechnol. 2011 May 15;29(7):644-52. doi: 10.1038\/nbt.1883. PubMed PMID: 21572440.\",\n      ],\n    },\n}\n"
    }
]