Description

Downloads the required files for either Nr or GTDB for building into a CAT database

Input

name:type
description
pattern

meta{:bash}

:map

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

db{:bash}

:string

Which database to download

nr|GTDB

Output

name:type
description
pattern

fasta{:bash}

meta{:bash}

:map

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

${prefix}/*.${db}.gz{:bash}

:file

FASTA file containing all the NCBI NR or GTDB sequences

*.${db}.gz

names{:bash}

meta{:bash}

:map

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

${prefix}/*.names.dmp{:bash}

:file

NCBI taxonomy-style names.dmp text file

*.names.dmp

nodes{:bash}

meta{:bash}

:map

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

${prefix}/*.nodes.dmp{:bash}

:file

NCBI taxonomy-style nodes.dmp text file

*.nodes.dmp

acc2tax{:bash}

meta{:bash}

:map

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

${prefix}/*accession2taxid*.gz{:bash}

:file

NCBI taxonomy names accession to taxonomy file

*accession2taxid*

log{:bash}

meta{:bash}

:map

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

${prefix}/*.log{:bash}

:file

Log file of the download process

*.log

versions_catpack{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

catpack{:bash}

:string

The tool name

CAT_pack --version | sed 's/CAT_pack pack v//g;s/ .*//g'{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

catpack{:bash}

:string

The name of the tool

CAT_pack --version | sed 's/CAT_pack pack v//g;s/ .*//g'{:bash}

:eval

The expression to obtain the version of the tool

Tools

catpack
MIT

CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)

github.com/MGXlab/CAT_pack 10.1186/s13059-019-1817-x
included in
magseqsubmit
maintainer
Github user jfy133
get in touch
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