name: bedtools_maskfasta description: masks sequences in a FASTA file based on intervals defined in a feature file. keywords: - bed - fasta - maskfasta tools: - bedtools: description: | A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html licence: ["MIT"] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - bed: type: file description: Bed feature file pattern: "*.{bed}" - fasta: type: file description: Input fasta file pattern: "*.{fa,fasta}" output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - fasta: type: file description: Output masked fasta file pattern: "*.{fa}" - versions: type: file description: File containing software versions pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh"