genomescope.yaml 4.07 KB
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{
  id: genomescope,
  name: GenomeScope,
  article: "10.1093/bioinformatics/btx153",
  website: "http://qb.cshl.edu/genomescope/",
  git: "https://github.com/schatzlab/genomescope",
  description: "Fast genome analysis from unassembled short reads",
  version: "1.0.0",
  documentation: "https://github.com/schatzlab/genomescope/blob/master/README.md",
  multiqc: "custom",
  commands:
    [
      {
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        name: jellyfish_count,
        command: jellyfish count,
        output_dir: jellyfish,
        inputs: [{ name: reads , file: ""}],
        outputs: [{ name: kmer_counts, file: counts.jf, description: "Jellyfish kmer counts file" }],
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        options:
          [
            {
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              name: jellyfish_threads,
              prefix: -t,
              type: numeric,
              value: 4,
              min: 1,
              max: NA,
              step: 1,
              label: "Number of threads to use",
            },
            {
              name: jellyfish_count_canonical_kmer,
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              prefix: ,
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              type: checkbox,
              value: TRUE,
              label: "-C : Save in the hash only canonical k-mers, while the count is the number of occurrences of both a k-mer and it reverse complement",
            },
            {
              name: jellyfish_count_kmer_len,
              prefix: -m,
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              type: numeric,
              value: 21,
              min: 1,
              max: NA,
              step: 1,
              label: "K-mers length",
            },
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            {
              name: jellyfish_count_hash_size,
              prefix: -s,
              type: numeric,
              value: 100000000,
              min: 1,
              max: NA,
              step: 1,
              label: "Kmer size estimation",
            },
          ]
      },
      {
        name: jellyfish_histo,
        command: jellyfish histo,
        output_dir: jellyfish,
        inputs: [{ name: kmer_counts , file: "counts.jf"}],
        outputs: [{ name: kmer_histo, file: kmer_histo_jf.hist, description: "Jellyfish kmer histogram" }],
        options:
          [
            {
              name: jellyfish_threads,
              prefix: -t,
              type: numeric,
              value: 4,
              min: 1,
              max: NA,
              step: 1,
              label: "Number of threads to use",
            },
          ]
      },
      {
        name: genomescope,
        command: Rscript /opt/biotools/genomescope.R,
        output_dir: genomescope,
        inputs: [{ name: kmer_histo , file: "kmer_histo_jf.hist"}],
        outputs: [
          { name: GenomeScope_Profile, file: "/GenomeScope_Profile_mqc.png", description: "Genome profile graph" },
          { name: GenomeScope_Profile_log_scale, file: "/GenomeScope_Profile_log_scale_mqc.png", description: "Genome profile graph (log scale)" },
          { name: Summary, file: "/GenomeScope_Summary_mqc.tsv", description: "GenomeScope summary table" }
        ],
        options:
          [
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            {
              name: genomescope_reads_len,
              prefix: ,
              type: numeric,
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              value: 150,
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              min: 1,
              max: NA,
              step: 1,
              label: "Read length",
            },
          ]
      },
    ],
  install:  {
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    jellyfish: [
      "cd /opt/biotools/bin",
      "wget -O jellyfish https://github.com/gmarcais/Jellyfish/releases/download/v2.3.0/jellyfish-linux",
      "chmod +x /opt/biotools/bin/jellyfish"
    ],
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    genomescope: [
      "cd /opt/biotools",
      "wget -O genomescope.tar.gz https://github.com/schatzlab/genomescope/archive/v1.0.0.tar.gz",
      "tar -xvzf genomescope.tar.gz",
      "mv genomescope-1.0.0/genomescope.R .",
      "rm -r genomescope-1.0.0 genomescope.tar.gz"
    ],
  },
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  citations: [
    genomescope: [
      "Gregory W Vurture, Fritz J Sedlazeck, Maria Nattestad, Charles J Underwood, Han Fang, James Gurtowski, Michael C Schatz, GenomeScope: fast reference-free genome profiling from short reads, Bioinformatics, Volume 33, Issue 14, 15 July 2017, Pages 2202–2204, https://doi.org/10.1093/bioinformatics/btx153"
    ]
  ]
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}