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, fasta, fna}"
  - databases:
      type: directory
      description: |
        Downloaded AntiSMASH databases (e.g. in the AntiSMASH installation directory
        "data/databases")
      pattern: "*/"
  - antismash_dir:
      type: directory
      description: |
        A local copy of an AntiSMASH installation folder. This is required when running with
        docker and singularity (not required for conda), due to attempted 'modifications' of
        files during database checks in the installation directory, something that cannot
        be done in immutable docker/singularity containers. Therefore, a local installation
        directory needs to be mounted (including all modified files from the downloading step)
        to the container as a workaround.
      pattern: "*/"
  - gff:
      type: file
      description: Annotations in GFF3 format (only if sequence_input is in FASTA format)
      pattern: "*.gff"

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"
  - html_accessory_files:
      type: directory
      description: Accessory files for the HTML output
      pattern: "{css/,images/,js/}"
  - knownclusterblast_html:
      type: file
      description: Tables with MIBiG hits in HTML format
      pattern: "knownclusterblast/region*/ctg*.html"
  - knownclusterblast_dir:
      type: directory
      description: Directory with MIBiG hits
      pattern: "knownclusterblast/"
  - knownclusterblast_txt:
      type: file
      description: Tables with MIBiG hits
      pattern: "knownclusterblast/*_c*.txt"
  - svg_files_clusterblast:
      type: file
      description: SVG images showing the % identity of the aligned hits against their queries
      pattern: "svg/clusterblast*.svg"
  - svg_files_knownclusterblast:
      type: file
      description: SVG images showing the % identity of the aligned hits against their queries
      pattern: "svg/knownclusterblast*.svg"
  - gbk_input:
      type: file
      description: Nucleotide sequence and annotations in GenBank format; converted from input file
      pattern: "*.gbk"
  - json_results:
      type: file
      description: Nucleotide sequence and annotations in JSON format; converted from GenBank file (gbk_input)
      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 output folder in zip format
      pattern: "*.zip"
  - gbk_results:
      type: file
      description: Nucleotide sequence and annotations in GenBank 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 antiSMASH documentation "Annotation sideloading")
      pattern: "regions.js"

authors:
  - "@jasmezz"
