name: busco_busco
description: Benchmarking Universal Single Copy Orthologs
keywords:
  - quality control
  - genome
  - transcriptome
  - proteome
tools:
  - busco:
      description: BUSCO provides measures for quantitative assessment of genome assembly,
        gene set, and transcriptome completeness based on evolutionarily informed expectations
        of gene content from near-universal single-copy orthologs selected from OrthoDB.
      homepage: https://busco.ezlab.org/
      documentation: https://busco.ezlab.org/busco_userguide.html
      tool_dev_url: https://gitlab.com/ezlab/busco
      doi: "10.1007/978-1-4939-9173-0_14"
      licence: ["MIT"]
      identifier: biotools:busco
input:
  - - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'test', single_end:false ]
    - fasta:
        type: file
        description: Nucleic or amino acid sequence file in FASTA format.
        pattern: "*.{fasta,fna,fa,fasta.gz,fna.gz,fa.gz}"
        ontologies: []
  - mode:
      type: string
      description: The mode to run Busco in. One of genome, proteins, or transcriptome
      pattern: "{genome,proteins,transcriptome}"
  - lineage:
      type: string
      description: The BUSCO lineage to use, or "auto", "auto_prok" or "auto_euk" to
        automatically select lineage
  - busco_lineages_path:
      type: directory
      description: Path to local BUSCO lineages directory.
  - config_file:
      type: file
      description: Path to BUSCO config file.
      ontologies: []
  - clean_intermediates:
      type: boolean
      description: Flag to remove intermediate files.
output:
  batch_summary:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test' ]
      - "*-busco.batch_summary.txt":
          type: file
          description: Summary of all sequence files analyzed
          pattern: "*-busco.batch_summary.txt"
          ontologies: []
  short_summaries_txt:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test' ]
      - short_summary.*.txt:
          type: file
          description: Short Busco summary in plain text format
          pattern: "short_summary.*.txt"
          ontologies: []
  short_summaries_json:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test' ]
      - short_summary.*.json:
          type: file
          description: Short Busco summary in JSON format
          pattern: "short_summary.*.json"
          ontologies:
            - edam: http://edamontology.org/format_3464 # JSON
  log:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test' ]
      - "*-busco.log":
          type: file
          description: BUSCO main log
          pattern: "*-busco.log"
          ontologies: []
  full_table:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test' ]
      - "*-busco/*/run_*/full_table.tsv":
          type: file
          description: Full BUSCO results table
          pattern: "full_table.tsv"
          ontologies:
            - edam: http://edamontology.org/format_3475 # TSV
  missing_busco_list:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test' ]
      - "*-busco/*/run_*/missing_busco_list.tsv":
          type: file
          description: List of missing BUSCOs
          pattern: "missing_busco_list.tsv"
          ontologies:
            - edam: http://edamontology.org/format_3475 # TSV
  single_copy_proteins:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test' ]
      - "*-busco/*/run_*/single_copy_proteins.faa":
          type: file
          description: Fasta file of single copy proteins (transcriptome mode)
          pattern: "single_copy_proteins.faa"
          ontologies: []
  seq_dir:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test' ]
      - "*-busco/*/run_*/busco_sequences":
          type: directory
          description: BUSCO sequence directory
          pattern: "busco_sequences"
  translated_dir:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test' ]
      - "*-busco/*/translated_proteins":
          type: directory
          description: Six frame translations of each transcript made by the transcriptome
            mode
          pattern: "translated_dir"
  busco_dir:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test' ]
      - "*-busco":
          type: directory
          description: BUSCO lineage specific output
          pattern: "*-busco"
  downloaded_lineages:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test' ]
      - busco_downloads/lineages/*:
          type: directory
          description: Lineages downloaded by BUSCO when running the analysis, for example
            bacteria_odb12
          pattern: "busco_downloads/lineages/*"
  single_copy_faa:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test' ]
      - "*-busco/*/run_*/busco_sequences/single_copy_busco_sequences/*.faa":
          type: file
          description: Single copy .faa sequence files
          pattern: "*-busco/*/run_*/busco_sequences/single_copy_busco_sequences/*.faa"
          ontologies: []
  single_copy_fna:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test' ]
      - "*-busco/*/run_*/busco_sequences/single_copy_busco_sequences/*.fna":
          type: file
          description: Single copy .fna sequence files
          pattern: "*-busco/*/run_*/busco_sequences/single_copy_busco_sequences/*.fna"
          ontologies: []
  versions:
    - versions.yml:
        type: file
        description: File containing software versions
        pattern: "versions.yml"
        ontologies:
          - edam: http://edamontology.org/format_3750 # YAML
authors:
  - "@priyanka-surana"
  - "@charles-plessy"
  - "@mahesh-panchal"
  - "@muffato"
  - "@jvhagey"
  - "@gallvp"
maintainers:
  - "@priyanka-surana"
  - "@charles-plessy"
  - "@mahesh-panchal"
  - "@muffato"
  - "@jvhagey"
  - "@gallvp"
