Description

Standardise the output of a wide range of taxonomic profilers

Input

name:type
description
pattern

meta{:bash}

:map

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

profile{:bash}

:file

profiler output file (mandatory)

*

profiler{:bash}

:string

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

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

format{:bash}

:string

Type of output file to be generated

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

taxonomy{:bash}

:directory

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

*/

Output

name:type
description
pattern

standardised_profile{:bash}

meta{:bash}

:map

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

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

:file

Standardised taxonomic profile

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

versions{:bash}

versions.yml{:bash}

: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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