name: nanolyse description: DNA contaminant removal using NanoLyse keywords: - contaminant_removal tools: - nanolyse: description: | DNA contaminant removal using NanoLyse homepage: https://github.com/wdecoster/nanolyse documentation: https://github.com/wdecoster/nanolyse#nanolyse input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - fastq: type: file description: | Basecalled reads in FASTQ.GZ format pattern: "*.fastq.gz" - fasta: type: file description: | A reference fasta file against which to filter. pattern: "*.fasta" output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - fastq: type: file description: Reads with contaminants removed in FASTQ format pattern: "*.fastq.gz" - log: type: file description: Log of the Nanolyse run. pattern: "*.log" - version: type: file description: File containing software version pattern: "*.{version.txt}" authors: - "@yuukiiwa"