[
    {
        "id": "racon",
        "name": "Racon",
        "article": "10.1101\/gr.214270.116",
        "website": "https:\/\/github.com\/lbcb-sci\/racon",
        "git": "https:\/\/github.com\/lbcb-sci\/racon",
        "description": "Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads ",
        "version": "1.5.0",
        "documentation": "https:\/\/github.com\/lbcb-sci\/racon\/blob\/master\/README.md",
        "multiqc": "custom",
        "commands": [
            {
                "name": "racon",
                "cname": "Racon",
                "command": "racon",
                "category": "post_assembly",
                "output_dir": "racon",
                "inputs": [
                    {
                        "name": "reads",
                        "type": "reads"
                    },
                    {
                        "name": "overlaps",
                        "type": "paf.gz"
                    },
                    {
                        "name": "assembly",
                        "type": "contigs"
                    }
                ],
                "outputs": [
                    {
                        "name": "assembly_corrected",
                        "type": "contigs",
                        "file": "assembly_corrected.fasta",
                        "description": "Assembly corrected"
                    }
                ],
                "options": [
                    {
                        "name": "racon_threads",
                        "prefix": "-t",
                        "type": "numeric",
                        "value": 4,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "Number of threads to use"
                    }
                ]
            }
        ],
        "install": [],
        "citations": {
            "racon": [
                "Vaser, R., Sovi\u0107, I., Nagarajan, N., & \u0160iki\u0107, M. (2017). Fast and accurate de novo genome assembly from long uncorrected reads. Genome Research, 27(5), 737\u2011746. https:\/\/doi.org\/10.1101\/gr.214270.116 "
            ]
        },
        "yaml": "{\n  id: racon,\n  name: Racon,\n  article: \"10.1101\/gr.214270.116\",\n  website: \"https:\/\/github.com\/lbcb-sci\/racon\",\n  git: \"https:\/\/github.com\/lbcb-sci\/racon\",\n  description: \"Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads \",\n  version: \"1.5.0\",\n  documentation: \"https:\/\/github.com\/lbcb-sci\/racon\/blob\/master\/README.md\",\n  multiqc: \"custom\",\n  commands:\n    [\n\n      {\n        name: racon,\n        cname: \"Racon\",\n        command:  racon,\n        category: \"post_assembly\",\n        output_dir: racon,\n        inputs: [{ name: reads, type: \"reads\" }, { name: overlaps, type: \"paf.gz\" }, { name: assembly, type: \"contigs\" }],\n        outputs:\n        [\n          { name: assembly_corrected, type: \"contigs\", file: assembly_corrected.fasta , description: \"Assembly corrected\" }\n        ],\n        options:\n          [\n            {\n              name: racon_threads,\n              prefix: -t,\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      },\n    ],\n  install: {\n    # racon: [\n    #   \"cd \/opt\/biotools\",\n    #   \"wget -O racon.tar.gz https:\/\/github.com\/lbcb-sci\/racon\/releases\/download\/1.4.10\/racon-v1.4.10.tar.gz\",\n    #   \"tar -xvzf racon.tar.gz\",\n    #   \"cd racon-v1.4.10\",\n    #   \"cmake -DCMAKE_BUILD_TYPE=Release\",\n    #   \"make -j 10\",\n    #   \"cd ..\",\n    #   \"rm racon.tar.gz\",\n    #   \"ENV PATH \/opt\/biotools\/racon-v1.4.10\/bin:$PATH\"\n    # ]\n  },\n  citations:  {\n    racon: [\n      \"Vaser, R., Sovi\u0107, I., Nagarajan, N., & \u0160iki\u0107, M. (2017). Fast and accurate de novo genome assembly from long uncorrected reads. Genome Research, 27(5), 737\u2011746. https:\/\/doi.org\/10.1101\/gr.214270.116 \"\n    ]\n  }\n}\n"
    }
]