name: gunc_run description: Detection of Chimerism and Contamination in Prokaryotic Genomes keywords: - prokaryote - assembly - genome - quality control - chimeras tools: - gunc: description: Python package for detection of chimerism and contamination in prokaryotic genomes. homepage: https://grp-bork.embl-community.io/gunc/ documentation: https://grp-bork.embl-community.io/gunc/ tool_dev_url: https://github.com/grp-bork/gunc doi: "10.1186/s13059-021-02393-0" licence: ['GNU General Public v3 or later (GPL v3+)'] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - fasta: type: file description: FASTA file containing contig (bins) pattern: "*.fa" - db: type: file description: GUNC database file pattern: "*.dmnd" 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" - maxcss_levels_tsv: type: file description: Output file with scores for a taxonomic level with the highest CSS score pattern: "*.tsv" - all_levels_tsv: type: file description: Optional output file with results for each taxonomic level pattern: "*.tsv" authors: - "@jfy133"