name: "seqkit_stats"
description: simple statistics of FASTA/Q files
keywords:
  - seqkit
  - stats
tools:
  - "seqkit":
      description: Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.
      homepage: https://bioinf.shenwei.me/seqkit/usage/
      documentation: https://bioinf.shenwei.me/seqkit/usage/
      tool_dev_url: https://github.com/shenwei356/seqkit/
      doi: "10.1371/journal.pone.0163962"
      licence: ["MIT"]

input:
  - meta:
      type: map
      description: >
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - reads:
      type: file
      description: >
        Either FASTA or FASTQ files.
      pattern: "*.{fa,fna,faa,fasta,fq,fastq}[.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"
  - stats:
      type: file
      description: >
        Tab-separated output file with basic sequence statistics.
      pattern: "*.tsv"

authors:
  - "@Midnighter"