Build centrifuge database for taxonomic profiling
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
fasta
:file
Fasta file containing sequences to be used in centrifuge database.
*.{fasta,fna}
conversion_table
A tab-separated file with sequence ID to taxonomy ID mapping
*.{map}
taxonomy_tree
A \t|\t-separated file mapping taxonomy. Typically nodes.dmp from the NCBI taxonomy dump. Links taxonomy IDs to their parents
*.{dmp}
name_table
A ’|‘-separated file mapping taxonomy IDs to a name. Typically names.dmp from the NCBI taxonomy dump. Links taxonomy IDs to their scientific name
size_table
Optional list of taxonomic IDs and lengths of the sequences belonging to the same taxonomic IDs.
*
cf
${prefix}/
versions_centrifuge
${task.process}
:string
The name of the process
centrifuge
The name of the tool
centrifuge --version 2>&1 | sed '1!d;s/.* version //'
:eval
The expression to obtain the version of the tool
versions
Classifier for metagenomic sequences
