Description

Standardise the output of a wide range of taxonomic profilers

Input

Name (Type)
Description
Pattern

meta (map)

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

]

profile (file)

profiler output file (mandatory)

*

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)

*/

Output

Name (Type)
Description
Pattern

meta (map)

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

]

standardised_profile (file)

Standardised taxonomic profile

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

versions (file)

File containing software versions

versions.yml
included in
taxprofiler
maintainer
Github user Midnighter
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