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

standardised_profile

meta:map

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

]

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

Standardised taxonomic profile

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

versions

versions.yml:file

File containing software versions

versions.yml

Tools

taxpasta
Apache-2.0

TAXonomic Profile Aggregation and STAndardisation

taxpasta.readthedocs.io https://github.com/taxprofiler/taxpasta
included in
taxprofiler
maintainer
Github user Midnighter
get in touch
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