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)

*

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
author
Github user Midnighter
get in touch
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Tools

taxpasta
Apache-2.0

TAXonomic Profile Aggregation and STAndardisation

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