name: artic_guppyplex
description: Aggregates fastq files with demultiplexed reads
keywords:
  - artic
  - aggregate
  - demultiplexed reads
tools:
  - artic:
      description: ARTIC pipeline - a bioinformatics pipeline for working with virus sequencing data sequenced with nanopore
      homepage: https://artic.readthedocs.io/en/latest/
      documentation: https://artic.readthedocs.io/en/latest/
      tool_dev_url: https://github.com/artic-network/fieldbioinformatics
      doi: ""
      licence: ["MIT"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - fastq_dir:
      type: directory
      description: Directory containing the fastq files with demultiplexed reads
      pattern: "*"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - fastq:
      type: file
      description: Aggregated FastQ files
      pattern: "*.{fastq.gz}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@joseespinosa"
  - "@drpatelh"