name: "concoct_cutupfasta"
description: Cut up fasta file in non-overlapping or overlapping parts of equal length.
keywords:
  - contigs
  - fragment
  - mags
  - binning
  - fasta
  - cut
  - cut up
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 ]
  - fasta:
      type: file
      description: (Uncompressed) FASTA file containing contigs
      pattern: "*.{fasta,fna,fa,fas}"
  - bed:
      type: boolean
      description: Specify whether to generate a BED file describing where each contig was cut up

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: Cut up fasta file in non-overlapping or overlapping parts of equal length.
      pattern: "*.fasta"
  - bed:
      type: file
      description: Optional BED File containing locations on original contigs where they were cut up.
      pattern: "*.bed"

authors:
  - "@jfy133"
