[
    {
        "id": "compare_vcfs",
        "name": "Compare VCFs",
        "description": "Compare several VCF files",
        "version": "1.2.0",
        "website": "https:\/\/github.com\/CFSAN-Biostatistics\/vcftoolz",
        "git": "https:\/\/github.com\/CFSAN-Biostatistics\/vcftoolz",
        "documentation": "https:\/\/vcftoolz.readthedocs.io\/en\/latest\/",
        "article": "10.21105\/joss.01144",
        "multiqc": "custom",
        "commands": [
            {
                "name": "compare_vcfs",
                "command": "vcftoolz compare",
                "category": "vcf_postprocess",
                "output_dir": "compare_vcfs",
                "inputs": [
                    {
                        "name": "vcfsinDir",
                        "type": "vcfs_dir",
                        "list": true
                    }
                ],
                "outputs": [
                    {
                        "name": "stats",
                        "type": "txt",
                        "file": "stats.txt",
                        "description": "Results of vcftoolz compare"
                    }
                ],
                "options": [
                    {
                        "name": "compare_vcfs_truth",
                        "prefix": null,
                        "type": "checkbox",
                        "value": false,
                        "label": "Compare VCF files to a truth VCF (case of a benchmark with a known truth)"
                    },
                    {
                        "name": "compare_vcfs_truth_file",
                        "type": "input_file",
                        "value": "",
                        "label": "Path to a truth VCF"
                    }
                ]
            }
        ],
        "install": {
            "vcftoolz": [
                "pip3 install vcftoolz==1.2.0",
                "ENV PATH ~\/.local\/bin:$PATH"
            ],
            "poppler-utils": [
                "apt -y update && apt install -y poppler-utils"
            ]
        },
        "citations": {
            "vcftools": [
                "Davis, (2019). vcftoolz: a Python package for comparing and evaluating Variant Call Format files.. Journal of Open Source Software, 4(35), 1144, https:\/\/doi.org\/10.21105\/joss.01144"
            ]
        },
        "yaml": "{\n  id: compare_vcfs,\n  name: Compare VCFs,\n  description: \"Compare several VCF files\",\n  version: \"1.2.0\",\n  website: \"https:\/\/github.com\/CFSAN-Biostatistics\/vcftoolz\",\n  git: \"https:\/\/github.com\/CFSAN-Biostatistics\/vcftoolz\",\n  documentation: \"https:\/\/vcftoolz.readthedocs.io\/en\/latest\/\",\n  article: \"10.21105\/joss.01144\",\n  multiqc: \"custom\",\n  commands:\n    [\n      {\n        name: compare_vcfs,\n        command: vcftoolz compare,\n        category: \"vcf_postprocess\",\n        output_dir: compare_vcfs,\n        inputs: [{ name: vcfsinDir, type: \"vcfs_dir\", list: true }],\n        outputs: [\n          { name: \"stats\", type: \"txt\", file: \"stats.txt\", description: \"Results of vcftoolz compare\" }\n        ],\n        options:\n          [\n            {\n              name: compare_vcfs_truth,\n              prefix: ,\n              type: checkbox,\n              value: FALSE,\n              label: \"Compare VCF files to a truth VCF (case of a benchmark with a known truth)\",\n            },\n            {\n              name: compare_vcfs_truth_file,\n              type: input_file,\n              value: \"\",\n              label: \"Path to a truth VCF\",\n            },\n          ],\n      },\n    ],\n  install: {\n    vcftoolz: [\n      \"pip3 install vcftoolz==1.2.0\",\n      \"ENV PATH ~\/.local\/bin:$PATH\"\n    ],\n    poppler-utils: [ # pdftoppm (pdf to png)\n      \"apt -y update && apt install -y poppler-utils\"\n    ]\n  },\n  citations: {\n    vcftools: [\n      \"Davis, (2019). vcftoolz: a Python package for comparing and evaluating Variant Call Format files.. Journal of Open Source Software, 4(35), 1144, https:\/\/doi.org\/10.21105\/joss.01144\"\n    ]\n  }\n}\n"
    }
]