name: antismash_antismashlite
description: antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters.
keywords:
  - secondary metabolites
  - BGC
  - biosynthetic gene cluster
  - genome mining
  - NRPS
  - RiPP
  - antibiotics
  - prokaryotes
  - bacteria
  - eukaryotes
  - fungi
  - antismash

tools:
  - antismashlite:
      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:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - sequence_input:
      type: file
      description: nucleotide sequence file (annotated)
      pattern: "*.{gbk, gb, gbff, genbank, embl}"
  - databases:
      type: directory
      description: downloaded antismash databases e.g. data/databases
      pattern: "*"
  - 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 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"
  - 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 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: "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 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: "modules"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - clusterblast_file:
      type: file
      description: Output of ClusterBlast algorithm
      pattern: "clusterblast/*_c*.txt"
  - css_file:
      type: file
      description: Style sheet containing the formatting of HTML output
      pattern: "css/*.css"
  - image_directory:
      type: directory
      description: image files for web view of antiSMASH results
      pattern: "images"
  - javascript:
      type: file
      description: JavaScript files
      pattern: "js/*.js"
  - knownclusterblast_html:
      type: file
      description: Tables with MIBiG hits in HTML format
      pattern: "knownclusterblast/region*/ctg*.html"
  - knownclusterblast_txt:
      type: file
      description: Tables with MIBiG hits
      pattern: "knownclusterblast/*_c*.txt"
  - svg_files_clusterblast:
      type: file
      description: SVG image showing the % identity of the aligned hits against their queries
      pattern: "svg/clusterblast*.svg"
  - svg_files_knownclusterblast:
      type: file
      description: SVG image showing the % identity of the aligned hits against their queries
      pattern: "svg/knownclusterblast*.svg"
  - gbk_input:
      type: file
      description: Nucleotide sequence + annotations in GenBank file format; converted from input file
      pattern: "*.gbk"
  - json_results:
      type: file
      description: Simple representation of all detected areas during the antiSMASH run in JSON format
      pattern: "*.json"
  - log:
      type: file
      description: Contains all the logging output that antiSMASH produced during its run
      pattern: "*.log"
  - zip:
      type: file
      description: Contains a compressed version of the folder in zip format
      pattern: "*.zip"
  - gbk_results:
      type: file
      description: Nucleotide sequence + annotations in GenBank file format; one file per antiSMASH hit
      pattern: "*region*.gbk"
  - clusterblastoutput:
      type: file
      description: Raw BLAST output of known clusters previously predicted by antiSMASH using the built-in ClusterBlast algorithm
      pattern: "clusterblastoutput.txt"
  - html:
      type: file
      description: Graphical web view of results in HTML format
      patterN: "index.html"
  - knownclusterblastoutput:
      type: file
      description: Raw BLAST output of known clusters of the MIBiG database
      pattern: "knownclusterblastoutput.txt"
  - json_sideloading:
      type: file
      description: Sideloaded annotations of protoclusters and/or subregions (see documentation "Annotation sideloading")
      pattern: "regions.js"

authors:
  - "@jasmezz"