vcfparser.yaml 1.51 KB
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{
  id: vcfparser,
  name: VCFparser,
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  tool_step: "vcf_postprocess",
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  description: "Plot VCF stats",
  version: "",
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  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",
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  article: ~,
  multiqc: "custom",
  commands:
    [
      {
        name: vcfparser,
        command: bash /opt/biotools/vcfparser/parseVCF.sh,
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        category: "vcf_postprocess",
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        output_dir: vcfparser,
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        inputs: [{ name: vcfs, type: "vcf" }],
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        outputs: [
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            {name: vcf_plots_mqc, type: "tsv", file: "vcf_plots_mqc_list.tsv"}
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          #{ name: "List of plots files", file: "vcf_plots_mqc_list.tsv", description: "List of plots files generated and included in the final report" }
        ],
        options:
          [
          ],
      },
    ],
  install: {
    vcfparser: [
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      "cd /opt/biotools",
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      "git clone https://gitlab.mbb.univ-montp2.fr/khalid/vcfparser.git"
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    ],
    patchwork: [
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    #patchwork cran version is not available for R version 3.5.3  
    #"Rscript -e 'install.packages(\"patchwork\",Ncpus=8, clean=TRUE);library(\"patchwork\"))'"
      "Rscript -e 'devtools::install_github(\"thomasp85/patchwork\")'"
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    ],
    tidyverse: [
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      "Rscript -e 'install.packages(\"tidyverse\",Ncpus=8, clean=TRUE);'"
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    ],
    ggplot2: [
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      "Rscript -e 'install.packages(\"ggplot2\",Ncpus=8, clean=TRUE);'"
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    ]
  },
  citations:  {
    #vcfparser: [
    #  ""
    #],
  }
}