name: "concoct_extractfastabins"
description: Creates a FASTA file for each new cluster assigned by CONCOCT
keywords:
  - contigs
  - fragment
  - mags
  - binning
  - fasta
  - cut
  - cut up
  - bins
  - merge

tools:
  - "concoct":
      description: "Clustering cONtigs with COverage and ComposiTion"
      homepage: "https://concoct.readthedocs.io/en/latest/index.html"
      documentation: "https://concoct.readthedocs.io/en/latest/index.html"
      tool_dev_url: "https://github.com/BinPro/CONCOCT"
      doi: "10.1038/nmeth.3103"
      licence: "['FreeBSD']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - original_fasta:
      type: file
      description: Original input FASTA file to CONOCT cut_up_fasta
      pattern: "*.{fasta,fna,fa,fas}"
  - csv:
      type: boolean
      description: Output table of merge_cutup_clustering with new cluster assignments
      pattern: ".csv"

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: FASTA files containing CONCOCT predicted bin clusters, named numerically by CONCOCT cluster ID in a directory called `fasta_bins`
      pattern: "*.fa.gz"

authors:
  - "@jfy133"
