Description

Standardise and merge two or more taxonomic profiles into a single table

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

profiles (file)

A list of taxonomic profiler output files (typically in text format, mandatory)

*.{tsv,csv,arrow,parquet,biom}

profiler (string)

Name of the profiler used to generate the profile (mandatory)

bracken|centrifuge|diamond|ganon|kaiju|kmcp|kraken2|krakenuniq|megan6|metaphlan|motus

format (string)

Type of output file to be generated

tsv|csv|ods|xlsx|arrow|parquet|biom

taxonomy (directory)

Directory containing at a minimum nodes.dmp and names.dmp files (optional)

*/

samplesheet (file)

A samplesheet describing the sample name and a filepath to a taxonomic abundance profile that needs to be relative from the Nextflow work directory of the executed process. The profiles must be provided even if you give a samplesheet as argument (optional)

*.{tsv,csv,ods,xlsx,arrow,parquet}

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

versions (file)

File containing software versions

versions.yml

merged_profiles (file)

Output file with standardised multiple profiles in one go and have all profiles combined into a single table.

*.{tsv,csv,ods,xlsx,arrow,parquet,biom}
included in
taxprofiler
maintainers
Github user sofstam
Github user jfy133
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

taxpasta
Apache-2.0

TAXonomic Profile Aggregation and STAndardisation

taxpasta.readthedocs.io https://github.com/taxprofiler/taxpasta