[
    {
        "id": "vcfparser",
        "name": "VCFparser",
        "description": "Plot VCF stats",
        "version": "",
        "website": "https:\/\/gitlab.mbb.univ-montp2.fr\/khalid\/vcfparser",
        "git": "https:\/\/gitlab.mbb.univ-montp2.fr\/khalid\/vcfparser",
        "documentation": "https:\/\/gitlab.mbb.univ-montp2.fr\/khalid\/vcfparser",
        "article": null,
        "multiqc": "custom",
        "commands": [
            {
                "name": "vcfparser",
                "command": "bash \/opt\/biotools\/vcfmultisampleparser\/parseMultiSamplesVCF.sh",
                "category": "vcf_postprocess",
                "output_dir": "vcfparser",
                "inputs": [
                    {
                        "name": "vcf",
                        "type": "vcf"
                    }
                ],
                "outputs": [
                    {
                        "name": "vcf_stats",
                        "type": "tsv",
                        "file": "\/{sample}_vcfstats.txt",
                        "description": "VCF stats"
                    },
                    {
                        "name": "vcf_png",
                        "type": "png",
                        "file": "\/{sample}_vcf_plots_mqc.png",
                        "description": "PNG summary of VCF stats"
                    }
                ],
                "options": []
            }
        ],
        "install": [],
        "citations": [],
        "yaml": "{\n  id: vcfparser,\n  name: VCFparser,\n  description: \"Plot VCF stats\",\n  version: \"\",\n  website: \"https:\/\/gitlab.mbb.univ-montp2.fr\/khalid\/vcfparser\",\n  git: \"https:\/\/gitlab.mbb.univ-montp2.fr\/khalid\/vcfparser\",\n  documentation: \"https:\/\/gitlab.mbb.univ-montp2.fr\/khalid\/vcfparser\",\n  article: ~,\n  multiqc: \"custom\",\n  commands:\n    [\n      {\n        name: vcfparser,\n        #command: bash \/opt\/biotools\/vcfparser\/parseVCF.sh,\n        command: bash \/opt\/biotools\/vcfmultisampleparser\/parseMultiSamplesVCF.sh,\n        category: \"vcf_postprocess\",\n        output_dir: vcfparser,\n        inputs: [{ name: vcf, type: \"vcf\" }],\n        outputs: [\n          { name: vcf_stats, type: \"tsv\", file: \"\/{sample}_vcfstats.txt\", description: \"VCF stats\" },\n          { name: vcf_png, type: \"png\", file: \"\/{sample}_vcf_plots_mqc.png\", description: \"PNG summary of VCF stats\" },\n        ],\n        options:\n          [\n          ],\n      },\n    ],\n  install: {\n    # vcfparser: [\n    #   \"cd \/opt\/biotools\",\n    #   #\"git clone https:\/\/gitlab.mbb.univ-montp2.fr\/khalid\/vcfparser.git\"\n    #   \"git clone https:\/\/github.com\/BELKHIR\/vcfmultisampleparser.git\"\n    # ],\n    # patchwork: [\n    # #patchwork cran version is not available for R version 3.5.3  \n    # #\"Rscript -e 'install.packages(\\\"patchwork\\\",Ncpus=8, clean=TRUE);library(\\\"patchwork\\\"))'\"\n    #   \"Rscript -e 'devtools::install_github(\\\"thomasp85\/patchwork\\\")'\"\n    # ],\n    # tidyverse: [\n    #   \"Rscript -e 'install.packages(\\\"tidyverse\\\",Ncpus=8, clean=TRUE);'\"\n    # ],\n    # ggplot2: [\n    #   \"Rscript -e 'install.packages(\\\"ggplot2\\\",Ncpus=8, clean=TRUE);'\"\n    # ]\n  },\n  citations:  {\n    #vcfparser: [\n    #  \"\"\n    #],\n  }\n}\n"
    }
]