name: bedtools_maskfasta
description: masks sequences in a FASTA file based on intervals defined in a feature file.
keywords:
  - bed
  - fasta
  - maskfasta
tools:
  - bedtools:
      description: |
        A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
      documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html
      licence: ["MIT"]
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - bed:
      type: file
      description: Bed feature file
      pattern: "*.{bed}"
  - fasta:
      type: file
      description: Input fasta file
      pattern: "*.{fa,fasta}"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - fasta:
      type: file
      description: Output masked fasta file
      pattern: "*.{fa}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@joseespinosa"
  - "@drpatelh"