name: "mash_screen" description: Screens query sequences against large sequence databases keywords: - screen - containment - contamination - taxonomic assignment tools: - "mash": description: Fast sequence distance estimator that uses MinHash homepage: https://github.com/marbl/Mash documentation: https://mash.readthedocs.io/en/latest/sketches.html tool_dev_url: https://github.com/marbl/Mash doi: "10.1186/s13059-016-0997-x" licence: ["https://github.com/marbl/Mash/blob/master/LICENSE.txt"] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - query: type: file description: Query sequences pattern: "*.fastq.gz" - sequence_sketch: type: file description: Sequence files to match against pattern: "*.msh" output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - versions: type: file description: File containing software versions pattern: "versions.yml" - screen: type: file description: List of sequences from fastx_db similar to query sequences pattern: "*.screen" authors: - "@mahesh-panchal"