modules/taxpasta_standardise

Standardise the output of a wide range of taxonomic profilers

taxonomic profilestandardisestandardisationmetagenomicstaxonomic profilingotu tablestaxon tables

https://github.com/nf-core/modules/[...]/modules/nf-core/taxpasta/standardise

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:false ]

`profile:file`

profiler output file (mandatory)

*

`profiler:string`

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

`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:false ]

`*.{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

modules/taxpasta_standardise

Description

Input

meta:map

profile:file

profiler:string

format:string

taxonomy:directory

Output

standardised_profile

meta:map

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

versions

versions.yml:file

Tools

taxpasta Apache-2.0

`meta:map`

`profile:file`

`profiler:string`

`format:string`

`taxonomy:directory`

`standardised_profile`

`meta:map`

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

`versions`

`versions.yml:file`

taxpasta
Apache-2.0