[
    {
        "id": "vcf2gds",
        "name": "vcf to gds",
        "article": "",
        "website": "",
        "git": "",
        "description": "Conversion of an vcf file to gds format with seqArray R package",
        "version": "",
        "documentation": "",
        "multiqc": "custom",
        "commands": [
            {
                "name": "vcf2gds",
                "command": "",
                "category": "format_conversion",
                "output_dir": "vcf2gds",
                "inputs": [
                    {
                        "name": "vcfFile",
                        "type": "vcf_file",
                        "description": "A vcf file to convert"
                    }
                ],
                "outputs": [
                    {
                        "name": "gds",
                        "type": "gds",
                        "file": "*.gds",
                        "description": "gds file"
                    }
                ],
                "options": [
                    {
                        "name": "vcf2gds_ld_trim",
                        "prefix": null,
                        "type": "checkbox",
                        "value": false,
                        "label": "Linkage Disequilibrium (LD) based SNP pruning with snpgdsLDpruning "
                    },
                    {
                        "name": "vcf2gds_min_maf",
                        "prefix": "--min-maf",
                        "type": "numeric",
                        "value": 0,
                        "min": 0,
                        "max": 0.5,
                        "step": 0.01,
                        "label": "if LD pruning : use the SNPs with >= maf only"
                    },
                    {
                        "name": "vcf2gds_ld_threshold",
                        "prefix": "--ld-threshold",
                        "type": "numeric",
                        "value": 1,
                        "min": 0,
                        "max": 1,
                        "step": 0.01,
                        "label": "if LD pruning : skip SNPs with ld > to this threshold"
                    },
                    {
                        "name": "vcf2gds_threads",
                        "prefix": "--threads",
                        "value": 16,
                        "min": 1,
                        "max": 64,
                        "step": 1,
                        "label": "Threads to use",
                        "type": "numeric"
                    }
                ]
            }
        ],
        "script": "vcf2gds.script.R",
        "install": [],
        "citations": {
            "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."
            ],
            "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. "
            ]
        },
        "yaml": "{\n  id: vcf2gds,\n  name: vcf to gds,\n  article: \"\",\n  website: \"\",\n  git: \"\",\n  description: \"Conversion of an vcf file to gds format with seqArray R package\",\n  version: \"\",\n  documentation: \"\",\n  multiqc: \"custom\",\n  commands:\n    [\n      {\n        name: vcf2gds,\n        command: \"\",\n        category: \"format_conversion\",\n        output_dir: vcf2gds,\n        inputs: [{ name: vcfFile, type: \"vcf_file\", description: \"A vcf file to convert\"} ],\n        outputs: [{ name: gds, type: \"gds\",file: \"*.gds\",  description: \"gds file\" }],\n        options: [\n          {\n              name: vcf2gds_ld_trim,\n              prefix: ,\n              type: checkbox,\n              value: FALSE,\n              label: \"Linkage Disequilibrium (LD) based SNP pruning with snpgdsLDpruning \",\n          },\n          {\n              name: vcf2gds_min_maf,\n              prefix: --min-maf,\n              type: numeric,\n              value: 0.00,\n              min: 0,\n              max: 0.5,\n              step: 0.01,\n              label: \"if LD pruning : use the SNPs with >= maf only\",\n          },\n          {\n              name: vcf2gds_ld_threshold,\n              prefix: --ld-threshold,\n              type: numeric,\n              value: 1,\n              min: 0,\n              max: 1,\n              step: 0.01,\n              label: \"if LD pruning : skip SNPs with ld > to this threshold\",\n          },\n          {\n              name: \"vcf2gds_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: vcf2gds.script.R,  \n  install:\n    {\n      # SeqArray: [\n      #   'Rscript -e ''if (!requireNamespace(\"BiocManager\", quietly = TRUE))  install.packages(\"BiocManager\");\n      #    BiocManager::install(\"SeqArray\", update = TRUE, ask = FALSE)'' '\n      # ],\n      # SNPRelate: [\n      #   'Rscript -e ''if (!requireNamespace(\"BiocManager\", quietly = TRUE))  install.packages(\"BiocManager\");\n      #    BiocManager::install(\"SNPRelate\", update = TRUE, ask = FALSE)'' '\n      # ]\n    },\n  citations:\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     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    },\n}\n"
    }
]