[
    {
        "id": "octopus",
        "name": "octopus",
        "article": "https:\/\/doi.org\/10.1038\/s41587-021-00861-3",
        "website": "https:\/\/github.com\/ekg\/octopus",
        "git": "https:\/\/github.com\/ekg\/octopus",
        "description": "Bayesian haplotype-based mutation calling",
        "version": "0.7.4",
        "documentation": "https:\/\/github.com\/luntergroup\/octopus\/wiki",
        "multiqc": "custom",
        "commands": [
            {
                "name": "octopus",
                "cname": "octopus",
                "command": "octopus",
                "category": "variant_calling",
                "output_dir": "octopus",
                "inputs": [
                    {
                        "name": "genome_fasta",
                        "type": "contigs",
                        "description": "Fasta reference",
                        "from": "parameter"
                    },
                    {
                        "name": "bams",
                        "type": "bams"
                    }
                ],
                "outputs": [
                    {
                        "name": "vcf",
                        "type": "vcf",
                        "file": "{sample}_output.vcf.gz",
                        "description": "Variant file"
                    }
                ],
                "options": [
                    {
                        "name": "octopus_genome_fasta",
                        "type": "input_file",
                        "value": "",
                        "label": "Path to reference genome fasta file"
                    },
                    {
                        "name": "octopus_threads",
                        "prefix": "--threads",
                        "type": "numeric",
                        "value": 4,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "Number of threads to use"
                    }
                ]
            }
        ],
        "install": [],
        "citations": {
            "octopus": [
                "Cooke, D.P., Wedge, D.C. & Lunter, G. A unified haplotype-based method for accurate and comprehensive variant calling. Nat Biotechnol (2021). https:\/\/doi.org\/10.1038\/s41587-021-00861-3"
            ],
            "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"
            ]
        },
        "yaml": "{\n  id: octopus,\n  name: octopus,\n  article: \"https:\/\/doi.org\/10.1038\/s41587-021-00861-3\",\n  website: \"https:\/\/github.com\/ekg\/octopus\",\n  git: \"https:\/\/github.com\/ekg\/octopus\",\n  description: \"Bayesian haplotype-based mutation calling\",\n  version: \"0.7.4\",\n  documentation: \"https:\/\/github.com\/luntergroup\/octopus\/wiki\",\n  multiqc: \"custom\",\n  commands:\n    [\n      {\n        name: octopus,\n        cname: \"octopus\",\n        command: octopus,\n        category: variant_calling,\n        output_dir: octopus,\n        inputs: [ \n                  { name: \"genome_fasta\", type: \"contigs\", description: \"Fasta reference\", from: \"parameter\" },\n                  { name: bams, type: \"bams\"}\n                ],\n        outputs: [\n          { name: vcf, type: \"vcf\", file: \"{sample}_output.vcf.gz\", description: \"Variant file\" },\n          \n        ],\n        options:\n          [\n            {\n              name: octopus_genome_fasta,\n              type: input_file,\n              value: \"\",\n              label: \"Path to reference genome fasta file\",\n            },\n            {\n              name: octopus_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\",\n            },\n          ],\n      },\n    ],\n  install: {\n      # mini-conda: [\n      # \"cd \/opt\/biotools\/bin && wget https:\/\/repo.continuum.io\/miniconda\/Miniconda3-latest-Linux-x86_64.sh\",\n      # \"bash Miniconda3-latest-Linux-x86_64.sh -b -p \/opt\/biotools\/conda \",\n      # \"ENV PATH $PATH:\/opt\/biotools\/conda\/bin\" ,\n      # \"echo 'export PATH=\/opt\/biotools\/conda\/bin:$PATH' >> \/etc\/environment\"\n      # ],\n      # octopus: [\n      #     \"conda install -y -c conda-forge -c bioconda octopus\"\n      #   ],\n      # tabix: [\n      #     \"apt -y update && apt install -y tabix\"\n      #   ]  \n    },\n  citations:  {\n    octopus: [\n      \"Cooke, D.P., Wedge, D.C. & Lunter, G. A unified haplotype-based method for accurate and comprehensive variant calling. Nat Biotechnol (2021). https:\/\/doi.org\/10.1038\/s41587-021-00861-3\"\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  }\n}\n"
    }
]