name: metabat2_metabat2
keywords:
  - sort
  - binning
  - depth
  - bam
  - coverage
  - de novo assembly
tools:
  - metabat2:
      description: Metagenome binning
      homepage: https://bitbucket.org/berkeleylab/metabat/src/master/
      documentation: https://bitbucket.org/berkeleylab/metabat/src/master/
      tool_dev_url: https://bitbucket.org/berkeleylab/metabat/src/master/
      doi: "10.7717/peerj.7359"
      licence: ["BSD-3-clause-LBNL"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - fasta:
      type: file
      description: Fasta file of the assembled contigs
      pattern: "*.{fa,fas,fasta,fna,fa.gz,fas.gz,fasta.gz,fna.gz}"
  - depth:
      type: file
      description: |
        Optional text file listing the coverage per contig pre-generated
        by metabat2_jgisummarizebamcontigdepths
      pattern: "*.txt"

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"
  - fasta:
      type: file
      description: Bins created from assembled contigs in fasta file
      pattern: "*.fa.gz"
  - tooshort:
      type: file
      description: Contigs that did not pass length filtering
      pattern: "*.tooShort.fa.gz"
  - lowdepth:
      type: file
      description: Contigs that did not have sufficient depth for binning
      pattern: "*.lowDepth.fa.gz"
  - unbinned:
      type: file
      description: Contigs that pass length and depth filtering but could not be binned
      pattern: "*.unbinned.fa.gz"
  - membership:
      type: file
      description: cluster memberships as a matrix format.
      pattern: "*.tsv.gz"

authors:
  - "@maxibor"
  - "@jfy133"
