name: 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"]

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}"
  - lineage:
      type: value
      description: The BUSCO lineage to use, or "auto" 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.

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - batch_summary:
      type: file
      description: Summary of all sequence files analyzed
      pattern: "*-busco.batch_summary.txt"
  - short_summaries_txt:
      type: file
      description: Short Busco summary in plain text format
      pattern: "short_summary.*.txt"
  - short_summaries_json:
      type: file
      description: Short Busco summary in JSON format
      pattern: "short_summary.*.json"
  - busco_dir:
      type: directory
      description: BUSCO lineage specific output
      pattern: "*-busco"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@priyanka-surana"
  - "@charles-plessy"
  - "@mahesh-panchal"
  - "@muffato"
  - "@jvhagey"