name: checkm_lineagewf description: CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. keywords: - checkm - mag - metagenome - quality - isolates - microbes - single cells - completeness - contamination - bins - genome bins tools: - checkm: description: Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes. homepage: https://ecogenomics.github.io/CheckM/ documentation: https://github.com/Ecogenomics/CheckM/wiki tool_dev_url: https://github.com/Ecogenomics/CheckM doi: "10.1101/gr.186072.114" licence: ['GPL v3'] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - fasta: type: file description: One or a list of multiple FASTA files of each bin, with extension defined with the fasta_ext value pattern: "*.{$fasta_ext}" - fasta_ext: type: value description: The file-type extension suffix of the input FASTA files (e.g., fasta, fna, fa, fas) output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'sample', bin:'1' ] - versions: type: file description: File containing software versions pattern: "versions.yml" - checkm_output: type: directory description: CheckM output directory pattern: "*/" - checkm_tsv: type: file description: CheckM summary completeness statistics table pattern: "*.tsv" authors: - "@jfy133"