blast_refseq.yaml 2.41 KB
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{
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  id: blast_refseq,
  name: blast refseq,
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  article: 10.1186/1471-2105-10-421,
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  website: "https://www.ncbi.nlm.nih.gov/genome/viruses/",
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  git: "",
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  description: "Blast fasta sequences on NCBI refseq viral database.",
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  version: "2.6.0-1",
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  documentation: "https://www.ncbi.nlm.nih.gov/genome/viruses/",
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  multiqc:  "custom",
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  commands:
    [
      {
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        name: blast_refseq,
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        cname: "Blast refseq",
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        command:  blastn,
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        category: "blast",
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        output_dir: blast_refseq,
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        inputs: [
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          { name: query, type: "fasta" }
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        ],
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        outputs:
        [
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          { name: blastout, type: "tsv", file: "blastout_mqc.tsv", description: "Top X tabular blast output" },
          { name: top_contigs, type: "fasta", file: "top_contigs.fasta", description: "Top X contigs fasta sequences" },
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        ],
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        options:
          [
            {
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              name: blast_refseq_threads,
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              prefix: -cpu,
              type: numeric,
              value: 4,
              min: 1,
              max: NA,
              step: 1,
              label: "Number of threads to use",
            },
            {
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              name: blast_refseq_evalue,
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              prefix: ,
              type: numeric,
              value: 1,
              min: 0,
              max: NA,
              step: 0.01,
              label: "e-value",
            },
            {
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              name: blast_refseq_max_target_sequences,
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              prefix: ,
              type: numeric,
              value: 1,
              min: 1,
              max: NA,
              step: 1,
              label: "max target sequence",
            },
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            {
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              name: blast_refseq_min_len,
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              prefix: ,
              type: numeric,
              value: 800,
              min: 0,
              max: NA,
              step: 10,
              label: "Blast min align length",
            },
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          ],
      },
    ],
  install: {
    blast:
    [
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      "apt -y update && apt install -y blast2=1:2.6.0-1"
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    ],
    mbb_mqc_plugin:
    [
      "cd /opt/biotools",
      "git clone https://gitlab.mbb.univ-montp2.fr/mmassaviol/mbb_mqc_plugin.git",
      "cd mbb_mqc_plugin",
      "python3 setup.py install"
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    ]
  },
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  citations:  {
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    blast: [
      "Camacho, C., Coulouris, G., Avagyan, V. et al. BLAST+: architecture and applications. BMC Bioinformatics 10, 421 (2009). https://doi.org/10.1186/1471-2105-10-421"
    ]
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  }
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}