name: "bioawk"
description: Bioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats.
keywords:
  - bioawk
  - fastq
  - fasta
  - sam
  - file manipulation
  - awk
tools:
  - "bioawk":
      description: "BWK awk modified for biological data"
      homepage: "https://github.com/lh3/bioawk"
      documentation: "https://github.com/lh3/bioawk"
      tool_dev_url: "https://github.com/lh3/bioawk"

      licence: "['Free software license (https://github.com/lh3/bioawk/blob/master/README.awk#L1)']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - input:
      type: file
      description: Input sequence biological sequence file (optionally gzipped) to be manipulated via program specified in `$args`.
      pattern: "*.{bed,gff,sam,vcf,fastq,fasta,tab,bed.gz,gff.gz,sam.gz,vcf.gz,fastq.gz,fasta.gz,tab.gz}"

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"
  - output:
      type: file
      description: |
        Manipulated and gzipped version of input sequence file following program specified in `args`.
        File name will be what is specified in `$prefix`. Do not include `.gz` suffix in `$prefix`! Output files` will be gzipped for you!
      pattern: "*.gz"

authors:
  - "@jfy133"
