Aggregates fastq files with demultiplexed reads
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
fastq_dir{:bash}
:directory
Directory containing the fastq files with demultiplexed reads
*
fastq{:bash}
*.fastq.gz{:bash}
:file
Aggregated FastQ files
*.{fastq.gz}
versions_artic{:bash}
${task.process}{:bash}
:string
The name of the process
artic{:bash}
The name of the tool
artic -v 2>&1 | sed "s/^.*artic //; s/ .*$//"{:bash}
:eval
The expression to obtain the version of the tool
versions{:bash}
ARTIC pipeline - a bioinformatics pipeline for working with virus sequencing data sequenced with nanopore
