Description

Build centrifuge database for taxonomic profiling

Input

name:type
description
pattern

meta:map

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

]

fasta:file

Fasta file containing sequences to be used in centrifuge database.

*.{fasta,fna}

conversion_table:file

A tab-separated file with sequence ID to taxonomy ID mapping

*.{map}

taxonomy_tree:file

A \t|\t-separated file mapping taxonomy. Typically nodes.dmp from the NCBI taxonomy dump. Links taxonomy IDs to their parents

*.{dmp}

name_table:file

A ’|‘-separated file mapping taxonomy IDs to a name. Typically names.dmp from the NCBI taxonomy dump. Links taxonomy IDs to their scientific name

*.{dmp}

size_table:file

Optional list of taxonomic IDs and lengths of the sequences belonging to the same taxonomic IDs.

*

Output

name:type
description
pattern

cf

meta:map

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

]

${prefix}/

${prefix}/:map

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

]

${prefix}/

versions

versions.yml:file

File containing software versions

versions.yml