name: "taxpasta_merge" description: Standardise and merge two or more taxonomic profiles into a single table keywords: - taxonomic profile - standardise - standardisation - metagenomics - taxonomic profiling - otu tables - taxon tables tools: - "taxpasta": description: "TAXonomic Profile Aggregation and STAndardisation" homepage: "https://taxpasta.readthedocs.io/" documentation: "https://taxpasta.readthedocs.io/" tool_dev_url: "https://github.com/taxprofiler/taxpasta" licence: "['Apache-2.0']" input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - profiles: type: file description: A list of taxonomic profiler output files (typically in text format, mandatory) pattern: "*.{tsv,csv,arrow,parquet,biom}" - samplesheet: type: file description: A samplesheet describing the sample name and a filepath to a taxonomic abundance profile that needs to be relative from the work environment. The profiles must be provided even if you give a samplesheet as argument (optional) pattern: "*.{tsv,csv,ods,xlsx,arrow,parquet}" - taxonomy: type: directory description: Directory containing at a minimum nodes.dmp and names.dmp files (optional) pattern: "*/" 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" - merged_profiles: type: file description: Output file with standardised multiple profiles in one go and have all profiles combined into a single table. pattern: "*.{tsv,csv,ods,xlsx,arrow,parquet,biom}" authors: - "@sofstam" - "@jfy133"