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}" - version: type: file description: File containing software version pattern: "*.{version.txt}" authors: - "@joseespinosa" - "@drpatelh"