name: antismash_antismashlitedownloaddatabases
description: antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters. This module downloads the antiSMASH databases.
keywords:
  - secondary metabolites
  - BGC
  - biosynthetic gene cluster
  - genome mining
  - NRPS
  - RiPP
  - antibiotics
  - prokaryotes
  - bacteria
  - eukaryotes
  - fungi
  - antismash
  - database
tools:
  - antismash:
      description: antiSMASH - the antibiotics and Secondary Metabolite Analysis SHell
      homepage: https://docs.antismash.secondarymetabolites.org
      documentation: https://docs.antismash.secondarymetabolites.org
      tool_dev_url: https://github.com/antismash/antismash
      doi: "10.1093/nar/gkab335"
      licence: ["AGPL v3"]

input:
  - database_css:
      type: directory
      description: |
        antismash/outputs/html/css folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by ther use by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
      pattern: "css"
  - database_detection:
      type: directory
      description: |
        antismash/detection folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
      pattern: "detection"
  - database_modules:
      type: directory
      description: |
        antismash/modules folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
      pattern: "modules"

output:
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

  - database:
      type: directory
      description: Download directory for antiSMASH databases
      pattern: "antismash_db"
  - css_dir:
      type: directory
      description: |
        antismash/outputs/html/css folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
      pattern: "css"
  - detection_dir:
      type: directory
      description: |
        antismash/detection folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
      pattern: "detection"
  - modules_dir:
      type: directory
      description: |
        antismash/modules folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
      pattern: "modules"

authors:
  - "@jasmezz"