[
    {
        "id": "multiSamplesvcfparser",
        "name": "multiSamplesvcfparser",
        "description": "Plot stats for a multisample VCF file",
        "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": "multiSamplesvcfparser",
                "command": "bash vcfmultisampleparser\/parseMultiSamplesVCF.sh",
                "category": "vcf_postprocess",
                "output_dir": "multiSamplesvcfparser",
                "inputs": [
                    {
                        "name": "vcf",
                        "type": "vcf_file"
                    }
                ],
                "outputs": [
                    {
                        "name": "vcf_stats",
                        "type": "tsv",
                        "file": "vcfstats.txt",
                        "description": "VCF stats"
                    }
                ],
                "options": [
                    {
                        "name": "multiSamplesvcfparser_threads",
                        "prefix": "--thread_number",
                        "type": "numeric",
                        "value": 8,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "Number of threads to use"
                    }
                ]
            }
        ],
        "install": [],
        "citations": [],
        "yaml": "{\n  id: multiSamplesvcfparser,\n  name: multiSamplesvcfparser,\n  description: \"Plot stats for a multisample VCF file\",\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: multiSamplesvcfparser,\n        #command: bash \/opt\/biotools\/vcfparser\/parseVCF.sh,\n        command: bash vcfmultisampleparser\/parseMultiSamplesVCF.sh,\n        category: \"vcf_postprocess\",\n        output_dir: multiSamplesvcfparser,\n        inputs: [{ name: vcf, type: \"vcf_file\" }],\n        outputs: [\n          { name: vcf_stats, type: \"tsv\", file: \"vcfstats.txt\", description: \"VCF stats\" },\n        ],\n        options:\n          [\n          {\n              name: multiSamplesvcfparser_threads,\n              prefix: --thread_number,\n              type: numeric,\n              value: 8,\n              min: 1,\n              max: NA,\n              step: 1,\n              label: \"Number of threads to use\",\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    # doParallel: [\n    #   \"Rscript -e 'install.packages(\\\"doParallel\\\",Ncpus=8, clean=TRUE);'\"\n    # ]\n  },\n  citations:  {\n    #vcfparser: [\n    #  \"\"\n    #],\n  }\n}\n"
    }
]