Description

Aggregates fastq files with demultiplexed reads

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

fastq_dir:directory

Directory containing the fastq files with demultiplexed reads

*

Output

name:type
description
pattern

fastq

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.fastq.gz:file

Aggregated FastQ files

*.{fastq.gz}

versions

versions.yml:file

File containing software versions

versions.yml

Tools

artic
MIT

ARTIC pipeline - a bioinformatics pipeline for working with virus sequencing data sequenced with nanopore