Description

Convert taxon names to TaxIds

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

name:string

Taxon name to look up (provide either this or names.txt, not both)

names_txt:file

File with taxon names to look up, each on their own line (provide either this or name, not both)

taxdb:file

Taxonomy database unpacked from ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz

Output

name:type
description
pattern

tsv

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*.tsv:file

TSV file of Taxon names and their taxon ID

*.tsv

versions

versions.yml:file

File containing software versions

versions.yml