Build centrifuger database for taxonomic profiling
Input
name:type
description
pattern
meta
:map
Groovy Map containing sample information. e.g. [id:'test', single_end:false ]
references
:file
One or more reference genome sequence files in FASTA format.
These are staged into the work directory and used to generate.a renference list file (used with -l option).
taxonomy_nodes
:file
File describing parent-child relationships of a taxonomic tree in NCBI nodes.dmp format
taxonomy_names
:file
File describing individual members of a taxonomic tree in NCBI names.dmp format
conversion_table
:file
Required: a tab-seperated file, mapping sequence IDs to taxonomy IDs.
Output
name:type
description
pattern
db
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
${prefix}
:directory
Centrifuger database index files
${prefix}
versions_centrifuger
${task.process}
:string
The name of the process
centrifuger
:string
The name of the tool
centrifuger -v 2>&1 | sed 's/Centrifuger v//'
:eval
The expression to obtain the version of the tool
Topics
name:type
description
pattern
versions
${task.process}
:string
The name of the process
centrifuger
:string
The name of the tool
centrifuger -v 2>&1 | sed 's/Centrifuger v//'
:eval
The expression to obtain the version of the tool
Tools
centrifuger
MIT
Lossless compression of microbial genomes for efficient and accurate metagenomic sequence classification.
