[
    {
        "id": "medaka",
        "name": "medaka",
        "article": "",
        "website": "https:\/\/github.com\/nanoporetech\/medaka",
        "git": "https:\/\/github.com\/nanoporetech\/medaka",
        "description": "Medaka is a tool to create a consensus sequence of nanopore sequencing data.",
        "version": "1.8.0",
        "documentation": "https:\/\/nanoporetech.github.io\/medaka\/",
        "multiqc": "custom",
        "commands": [
            {
                "name": "medaka",
                "cname": "Medaka",
                "command": "medaka_consensus",
                "category": "post_assembly",
                "output_dir": "medaka",
                "inputs": [
                    {
                        "name": "read",
                        "type": "reads"
                    },
                    {
                        "name": "assembly_fasta",
                        "type": "contigs"
                    }
                ],
                "outputs": [
                    {
                        "name": "consensus_assembly",
                        "type": "contigs",
                        "file": "consensus.fasta",
                        "description": "Consensus assembly file"
                    }
                ],
                "options": [
                    {
                        "name": "medaka_threads",
                        "prefix": "-t",
                        "type": "numeric",
                        "value": 4,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "Number of threads to use"
                    },
                    {
                        "name": "medaka_model",
                        "type": "select",
                        "choices": [
                            {
                                "r941_trans": "r941_trans"
                            },
                            {
                                "r941_flip213": "r941_flip213"
                            },
                            {
                                "r941_flip235": "r941_flip235"
                            },
                            {
                                "r941_min_fast": "r941_min_fast"
                            },
                            {
                                "r941_min_high": "r941_min_high"
                            },
                            {
                                "r941_prom_fast": "r941_prom_fast"
                            },
                            {
                                "r941_prom_high": "r941_prom_high"
                            }
                        ],
                        "value": "r941_min_high",
                        "label": "Medaka model"
                    }
                ]
            }
        ],
        "install": [],
        "citations": {
            "medaka": [
                "medaka: Sequence correction provided by ONT Research. https:\/\/github.com\/nanoporetech\/medaka"
            ],
            "minimap2": [
                "Heng Li, Minimap2: pairwise alignment for nucleotide sequences, Bioinformatics, Volume 34, Issue 18, 15 September 2018, Pages 3094-3100, https:\/\/doi.org\/10.1093\/bioinformatics\/bty191"
            ],
            "tabix": [
                "Heng Li, Tabix: fast retrieval of sequence features from generic TAB-delimited files, Bioinformatics, Volume 27, Issue 5, 1 March 2011, Pages 718-719, https:\/\/doi.org\/10.1093\/bioinformatics\/btq671"
            ],
            "samtools": [
                "Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, 1000 Genome Project Data Processing Subgroup, The Sequence Alignment\/Map format and SAMtools, Bioinformatics, Volume 25, Issue 16, 15 August 2009, Pages 2078-2079, https:\/\/doi.org\/10.1093\/bioinformatics\/btp352"
            ]
        },
        "yaml": "{\n  id: medaka,\n  name: medaka,\n  article: \"\",\n  website: \"https:\/\/github.com\/nanoporetech\/medaka\",\n  git: \"https:\/\/github.com\/nanoporetech\/medaka\",\n  description: \"Medaka is a tool to create a consensus sequence of nanopore sequencing data.\",\n  version: \"1.8.0\",\n  documentation: \"https:\/\/nanoporetech.github.io\/medaka\/\",\n  multiqc: \"custom\",\n  commands:\n    [\n      {\n        name: medaka,\n        cname: \"Medaka\",\n        command:  medaka_consensus,\n        category: \"post_assembly\",\n        output_dir: medaka,\n        inputs: [ \n          {name: read, type: \"reads\" },\n          {name: assembly_fasta, type: \"contigs\" }\n        ],\n        outputs:\n        [\n          { name: consensus_assembly, type: \"contigs\" , file: \"consensus.fasta\" , description: \"Consensus assembly file\" }\n        ],\n        options:\n          [\n            {\n              name: medaka_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              name: medaka_model,\n              type: select,\n              choices: [\n                r941_trans: \"r941_trans\",\n                r941_flip213: \"r941_flip213\",\n                r941_flip235: \"r941_flip235\",\n                r941_min_fast: \"r941_min_fast\",\n                r941_min_high: \"r941_min_high\",\n                r941_prom_fast: \"r941_prom_fast\",\n                r941_prom_high: \"r941_prom_high\",\n              ],\n              value: \"r941_min_high\",\n              label: \"Medaka model\",\n            },\n          ],\n      },\n    ],\n  install: {\n    # htslib: [\n    #   \"wget -O htslib.tar.bz2 https:\/\/github.com\/samtools\/htslib\/releases\/download\/1.9\/htslib-1.9.tar.bz2\",\n    #   \"tar -xvjf htslib.tar.bz2\",\n    #   \"rm htslib.tar.bz2\",\n    #   \"cd htslib-1.9\",\n    #   \".\/configure\",\n    #   \"make -j 10\",\n    #   \"make install\"\n    # ],\n    # samtools: [\n    #   \"cd \/opt\/biotools\",\n    #   \"wget https:\/\/github.com\/samtools\/samtools\/releases\/download\/1.9\/samtools-1.9.tar.bz2\",\n    #   \"tar -xvjf samtools-1.9.tar.bz2\",\n    #   \"cd samtools-1.9\",\n    #   \".\/configure && make -j 10\",\n    #   \"cd ..\",\n    #   \"mv samtools-1.9\/samtools bin\/samtools\",\n    #   \"rm -r samtools-1.9 samtools-1.9.tar.bz2\"\n    # ],\n    # tabix: [\n    #   \"apt-get -y install tabix\"\n    # ],\n    # minimap2: [\n    #   \"cd \/opt\/biotools\",\n    #   \"wget https:\/\/github.com\/lh3\/minimap2\/releases\/download\/v2.17\/minimap2-2.17_x64-linux.tar.bz2\",\n    #   \"tar -xvjf minimap2-2.17_x64-linux.tar.bz2\",\n    #   \"rm minimap2-2.17_x64-linux.tar.bz2\",\n    #   \"ENV PATH \/opt\/biotools\/minimap2-2.17_x64-linux:$PATH\"\n    # ],\n    # biopython: [\n    #   \"pip3 install biopython==1.76\"\n    # ],\n    # medaka: [\n    #   \"pip3 install medaka==0.10.1\"\n    # ]\n  },\n  citations:  {\n    medaka: [\n      \"medaka: Sequence correction provided by ONT Research. https:\/\/github.com\/nanoporetech\/medaka\"\n    ],\n    minimap2: [\n      \"Heng Li, Minimap2: pairwise alignment for nucleotide sequences, Bioinformatics, Volume 34, Issue 18, 15 September 2018, Pages 3094-3100, https:\/\/doi.org\/10.1093\/bioinformatics\/bty191\"\n    ],\n    tabix: [\n      \"Heng Li, Tabix: fast retrieval of sequence features from generic TAB-delimited files, Bioinformatics, Volume 27, Issue 5, 1 March 2011, Pages 718-719, https:\/\/doi.org\/10.1093\/bioinformatics\/btq671\"\n    ],\n    samtools: [\n      \"Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, 1000 Genome Project Data Processing Subgroup, The Sequence Alignment\/Map format and SAMtools, Bioinformatics, Volume 25, Issue 16, 15 August 2009, Pages 2078-2079, https:\/\/doi.org\/10.1093\/bioinformatics\/btp352\"\n    ],\n    \n  }\n}\n"
    }
]