radsex_map.yaml

{
  id: radsex_map,
  name: radsex_map,
  article:  https://doi.org/10.1111/1755-0998.13360,
  website: "https://onlinelibrary.wiley.com/doi/full/10.1111/1755-0998.13360",
  git: "https://github.com/SexGenomicsToolkit/radsex",
  description: "Aligning markers to a genome and computing bias and probability of association with group for each aligned marker",
  version: "latest",
  documentation: "https://sexgenomicstoolkit.github.io/html/radsex/introduction.html",
  multiqc: "custom",
  commands:
    [
      {
        name: radsex_map,
        command: /opt/biotools/radsex/bin/radsex map,
        category: "radsex",
        output_dir: radsex_map,
        inputs: [
          { name: "markers_table", type: "tsv", file: "", description: "Table containing the depth of each marker in each individual (tabulated file)" },
          { name: "popmap_file", type: "popmap",  description: "Path to population tsv file" },
          { name: "genome_fasta", type: "contigs", description: "Fasta reference", from: "parameter"},
        ],
        outputs:
          [
            { name: map_results, type: "tsv", file: "map_results.tsv", description: "Alignment results indicating contig and contig position where the marker was mapped" }
          ],
        options:
          [
             {
              name: radsex_map_genome_fasta,
              prefix: "--genome-file",
              type: input_file,
              value: "",
              label: "Path to the genome file",
            },
            {
              name: radsex_map_chromosome_file,
              prefix: "",
              type: input_file,
              value: "",
              label: "Path to the chromosome file",
            },            
            {
              name: "radsex_map_min_quality",
              prefix: "--min-quality",
              value: 20,
              min: 1,
              max: NA,
              step: 1,
              label: "Minimum mapping quality to consider a marker properly aligned",
              type: "numeric",
            },
            {
              name: "radsex_map_min_frequency",
              prefix: "--min-frequency",
              value: 0.1,
              min: 0,
              max: 1,
              step: 0.1,
              label: "Minimum frequency of a marker in a population to retain it",
              type: "numeric",
            },
            {
              name: "radsex_map_min_depth",
              prefix: "--min-depth",
              value: 5,
              min: 1,
              max: NA,
              step: 1,
              label: "Minimum depth to consider a marker present in an individual",
              type: "numeric",
            },
            {
              name: "radsex_map_signif_threshold",
              prefix: "--signif-threshold",
              value: 0.05,
              min: 0,
              max: 1,
              step: 0.001,
              label: "P-value threshold to consider a marker significantly associated with a phenotypic group",
              type: "numeric",
            },
          ],
      },
    ],
  prepare_report_script:  radsex_map.prepare.report.R,
  prepare_report_outputs: [
    Marker_depth_radsex_map_mqc.png,
  ],
  install:
    {
      radsex_apt_dependencies: [
        "apt-get update",
        "apt-get install -y gcc zlib1g-dev pkg-config libfreetype6-dev libpng-dev"
      ],
      radsex: [
        "cd /opt/biotools",
        "git clone https://gitlab.mbb.univ-montp2.fr/khalid/radsex",
        "cd radsex",
        "make -j 10",
      ],
      sgtr: [
        'Rscript -e ''devtools::install_github("SexGenomicsToolkit/sgtr");library("sgtr")'''
      ],
    },
    citations:  {
      radsex: [
        "Feron, R., Pan, Q., Wen, M., Imarazene, B., Jouanno, E., Anderson, J., Herpin, A., et al. (2021), RADSex: A computational workflow to study sex determination using restriction site‐associated DNA sequencing data. Mol Ecol Resour. https://doi.org/10.1111/1755-0998.13360"
      ]
    }
}