[
    {
        "id": "Relatedness_gds",
        "name": "identity-by-descent IBD",
        "article": "",
        "website": "",
        "git": "",
        "description": "identity-by-descent (IBD) estimation in SNPRelate either with the method of moments (MoM) (Purcell et al., 2007) or maximum likelihood estimation (MLE) (Milligan, 2003; Choi et al., 2009)",
        "version": "",
        "documentation": "",
        "multiqc": "custom",
        "commands": [
            {
                "name": "Relatedness_gds",
                "command": "",
                "category": "genet_pop",
                "output_dir": "Relatedness_gds",
                "inputs": [
                    {
                        "name": "gds",
                        "type": "gds",
                        "file": "",
                        "description": "gds file"
                    }
                ],
                "outputs": [
                    {
                        "name": "k0",
                        "type": "txt",
                        "file": "*_k0.txt",
                        "description": "IBD coefficient, the probability of sharing ZERO IBD"
                    },
                    {
                        "name": "k1",
                        "type": "txt",
                        "file": "*_k1.txt",
                        "description": "IBD coefficient, the probability of sharing ONE IBD"
                    },
                    {
                        "name": "k0vsk1_png",
                        "type": "png",
                        "file": "K0vsK1_plot_mqc.png",
                        "description": "K0 vs K1 plot"
                    },
                    {
                        "name": "K1_heatmap_png",
                        "type": "png",
                        "file": "K1_heatmap_mqc.png",
                        "description": "A heatmap of K1 values"
                    }
                ],
                "options": [
                    {
                        "name": "Relatedness_gds_method",
                        "type": "radio",
                        "value": "MoM",
                        "choices": [
                            {
                                "Plink Method of Moment": "MoM"
                            },
                            {
                                "ML using EM algo": "EM"
                            },
                            {
                                "ML using downhill.simplex algo": "downhill.simplex"
                            }
                        ],
                        "label": "Method to calculate IBD coef."
                    },
                    {
                        "name": "Relatedness_gds_threads",
                        "prefix": "--threads",
                        "value": 16,
                        "min": 1,
                        "max": 64,
                        "step": 1,
                        "label": "Threads to use",
                        "type": "numeric"
                    }
                ]
            }
        ],
        "script": "Relatedness_gds.script.R",
        "install": [],
        "citations": {
            "SNPRelate": [
                "Zheng X, Levine D, Shen J, Gogarten S, Laurie C, Weir B (2012). A High-performance Computing Toolset for Relatedness and Principal Component Analysis of SNP Data. Bioinformatics, 28(24), 3326-3328. doi: 10.1093\/bioinformatics\/bts606. "
            ],
            "SeqArray": [
                "Zheng X, Gogarten S, Lawrence M, Stilp A, Conomos M, Weir B, Laurie C, Levine D (2017). SeqArray - A storage-efficient high-performance data format for WGS variant calls. Bioinformatics. doi: 10.1093\/bioinformatics\/btx145."
            ],
            "PLINK": [
                "Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ & Sham PC. 2007. PLINK: a toolset for whole-genome association and population-based linkage analysis. American Journal of Human Genetics, 81."
            ]
        },
        "yaml": "{\n  id: Relatedness_gds,\n  name: identity-by-descent IBD,\n  article: \"\",\n  website: \"\",\n  git: \"\",\n  description: \"identity-by-descent (IBD) estimation in SNPRelate either with the method of moments (MoM) (Purcell et al., 2007) or maximum likelihood estimation (MLE) (Milligan, 2003; Choi et al., 2009)\",\n  version: \"\",\n  documentation: \"\",\n  multiqc: \"custom\",\n  commands:\n    [\n      {\n        name: Relatedness_gds,\n        command: \"\",\n        category: \"genet_pop\",\n        output_dir: Relatedness_gds,\n        inputs: [{ name: gds, type: \"gds\", file: \"\",description: \"gds file\"} ,\n                ],\n        outputs: [\n          { name: k0, type: \"txt\", file: \"*_k0.txt\", description: \"IBD coefficient, the probability of sharing ZERO IBD\" },\n          { name: k1, type: \"txt\", file: \"*_k1.txt\", description: \"IBD coefficient, the probability of sharing ONE IBD\" },\n          { name: k0vsk1_png, type: \"png\", file: \"K0vsK1_plot_mqc.png\", description: \"K0 vs K1 plot\" },\n          { name: K1_heatmap_png, type: \"png\", file: \"K1_heatmap_mqc.png\", description: \"A heatmap of K1 values\" },\n\n          \n        ],\n        options: [\n          {\n              name: \"Relatedness_gds_method\",\n              type: \"radio\",\n              value: \"MoM\",\n              choices: [Plink Method of Moment: MoM, ML using EM algo: EM, ML using downhill.simplex algo: downhill.simplex],\n              label: \"Method to calculate IBD coef.\",\n          },\n          {\n              name: \"Relatedness_gds_threads\",\n              prefix: \"--threads\",\n              value: 16,\n              min: 1,\n              max: 64,\n              step: 1,\n              label: \"Threads to use\",\n              type: \"numeric\",\n          },\n        ],\n      },\n    ],\n  script: Relatedness_gds.script.R,\n  install:\n    {\n      # SNPRelate: [\n      #   'Rscript -e ''if (!requireNamespace(\"BiocManager\", quietly = TRUE))  install.packages(\"BiocManager\");\n      #    BiocManager::install(\"SNPRelate\", update = TRUE, ask = FALSE)'' '\n      # ],\n      # SeqArray: [\n      #   'Rscript -e ''if (!requireNamespace(\"BiocManager\", quietly = TRUE))  install.packages(\"BiocManager\");\n      #    BiocManager::install(\"SeqArray\", update = TRUE, ask = FALSE)'' '\n      # ], \n    },\n  citations:\n    {\n     SNPRelate: [\n       \"Zheng X, Levine D, Shen J, Gogarten S, Laurie C, Weir B (2012). A High-performance Computing Toolset for Relatedness and Principal Component Analysis of SNP Data. Bioinformatics, 28(24), 3326-3328. doi: 10.1093\/bioinformatics\/bts606. \" \n       ],\n     SeqArray: [\n       \"Zheng X, Gogarten S, Lawrence M, Stilp A, Conomos M, Weir B, Laurie C, Levine D (2017). SeqArray - A storage-efficient high-performance data format for WGS variant calls. Bioinformatics. doi: 10.1093\/bioinformatics\/btx145.\" \n       ],  \n     PLINK: [\n       \"Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ & Sham PC. 2007. PLINK: a toolset for whole-genome association and population-based linkage analysis. American Journal of Human Genetics, 81.\"\n     ] \n    },\n}\n"
    }
]