name: "fastawindows"
description: Quickly compute statistics over a fasta file in windows.
keywords:
  - genome
  - fasta
  - tsv
  - bed
tools:
  - "fastawindows":
      description: "fasta_windows is a tool written for Darwin Tree of Life chromosomal level genome assemblies. The executable takes a fasta formatted file and calculates some statistics of interest in windows"
      homepage: "https://github.com/tolkit/fasta_windows"
      documentation: "None"
      licence: "['MIT']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - fasta:
      type: file
      description: FASTA file
      pattern: "*.{fa,fasta,fna}"

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"
  - freq:
      type: file
      description: TSV file with frequencies and statistics
      pattern: "*.{tsv}"
  - mononuc:
      type: file
      description: TSV file with mononucleotide counts
      pattern: "*.{tsv}"
  - dinuc:
      type: file
      description: TSV file with dinucleotide counts
      pattern: "*.{tsv}"
  - trinuc:
      type: file
      description: TSV file with trinucleotide counts
      pattern: "*.{tsv}"
  - tetranuc:
      type: file
      description: TSV file with tetranucleotide counts
      pattern: "*.{tsv}"
authors:
  - "@muffato"