name: "diamond_blastp"
description: Performs protein BLAST searches using DIAMOND
keywords:
  - diamond
  - blastp
  - protein
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - fasta:
      type: file
      description: Input protein FASTA file
      pattern: "*.{fasta,fa}"
  - meta2:
      type: map
      description: |
        Groovy Map containing database information
        e.g. [ id:'nr' ]
  - db:
      type: file
      description: DIAMOND formatted database file
      pattern: "*.dmnd"
  - outfmt:
      type: value
      description: |
        Output format code (0, 5, 6, 100, 101, 102, or 103)
  - blast_columns:
      type: value
      description: |
        BLAST output columns (only used when outfmt is 6)
output:
  - outmeta:
      type: map
      description: |
        Groovy Map containing sample information and database id
  - blast:
      type: file
      description: BLAST format output (when outfmt is 0)
      pattern: "*.blast*"
  - xml:
      type: file
      description: XML format output (when outfmt is 5)
      pattern: "*.xml*"
  - txt:
      type: file
      description: Tabular format output (when outfmt is 6)
      pattern: "*.txt*"
  - daa:
      type: file
      description: DAA format output (when outfmt is 100)
      pattern: "*.daa"
  - sam:
      type: file
      description: SAM format output (when outfmt is 101)
      pattern: "*.sam*"
  - tsv:
      type: file
      description: TSV format output (when outfmt is 102)
      pattern: "*.tsv*"
  - paf:
      type: file
      description: PAF format output (when outfmt is 103)
      pattern: "*.paf*"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@danilodileo"
