[
    {
        "id": "freebayes",
        "name": "freebayes",
        "article": "arxiv.org\/abs\/1207.3907",
        "website": "https:\/\/github.com\/ekg\/freebayes",
        "git": "https:\/\/github.com\/ekg\/freebayes",
        "description": "Bayesian haplotype-based genetic polymorphism discovery and genotyping",
        "version": "1.3.6",
        "documentation": "https:\/\/github.com\/ekg\/freebayes",
        "multiqc": "custom",
        "commands": [
            {
                "name": "freebayes",
                "cname": "Freebayes",
                "command": "freebayes-parallel",
                "category": "variant_calling",
                "output_dir": "freebayes",
                "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": "freebayes_genome_fasta",
                        "type": "input_file",
                        "value": "",
                        "label": "Path to reference genome fasta file"
                    },
                    {
                        "name": "freebayes_threads",
                        "prefix": "--threads",
                        "type": "numeric",
                        "value": 4,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "Number of threads to use"
                    }
                ]
            }
        ],
        "install": [],
        "citations": {
            "freebayes": [
                "Garrison, E., & Marth, G. (2012). Haplotype-based variant detection from short-read sequencing. arXiv preprint arXiv:1207.3907."
            ],
            "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: freebayes,\n  name: freebayes,\n  article: arxiv.org\/abs\/1207.3907,\n  website: \"https:\/\/github.com\/ekg\/freebayes\",\n  git: \"https:\/\/github.com\/ekg\/freebayes\",\n  description: \"Bayesian haplotype-based genetic polymorphism discovery and genotyping\",\n  version: \"1.3.6\",\n  documentation: \"https:\/\/github.com\/ekg\/freebayes\",\n  multiqc: \"custom\",\n  commands:\n    [\n      {\n        name: freebayes,\n        cname: \"Freebayes\",\n        command: freebayes-parallel,\n        category: variant_calling,\n        output_dir: freebayes,\n        inputs: [ #{ name: genome_fasta, type: \"contigs\" }, \n                  { name: \"genome_fasta\", type: \"contigs\", description: \"Fasta reference\", from: \"parameter\" },\n                  { name: bams, type: \"bams\"}],\n        outputs: [\n          { name: vcf, type: \"vcf\", file: \"{sample}_output.vcf.gz\", description: \"Variant file\" },\n          #{ name: gvcf, file: output.g.vcf.gz, description: \"Genomic variant file\" }\n        ],\n        options:\n          [\n            {\n              name: freebayes_genome_fasta,\n              type: input_file,\n              value: \"\",\n              label: \"Path to reference genome fasta file\",\n            },\n            {\n              name: freebayes_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      # freebayes: [\n      #     \"cd \/opt\/biotools\/bin\",\n      #     \"wget https:\/\/github.com\/ekg\/freebayes\/releases\/download\/v1.3.1\/freebayes-v1.3.1 -O freebayes\",\n      #     \"chmod +x freebayes\",\n      #     \"cd \/opt\/biotools\/\",\n      #     \"git clone https:\/\/github.com\/freebayes\/freebayes.git\" #to get the accompaning scripts (freebayes-parallel ...)\n      #   ],\n      #   vcflib: [\n      #      \"conda install -y -c bioconda vcflib\"\n      #   ],\n      #   parallel: [\n      #      \"conda install -y -c bioconda parallel\"\n      #   ],\n      #   tabix:\n      #   [\n      #     \"apt -y update && apt install -y tabix\"\n      #   ]\n    },\n  citations:  {\n    freebayes: [\n      \"Garrison, E., & Marth, G. (2012). Haplotype-based variant detection from short-read sequencing. arXiv preprint arXiv:1207.3907.\"\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"
    }
]