modules/catpack_download

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

taxonomic classificationclassificationdatabasedownload

https://github.com/nf-core/modules/[...]/modules/nf-core/catpack/download

Description

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

Input

name:type

description

pattern

`meta`
`:map`

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

`db`
`:string`

Which database to download

nr|GTDB

Output

name:type

description

pattern

`fasta`

`meta`
`:map`

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

`${prefix}/*.${db}.gz`
`:file`

FASTA file containing all the NCBI NR or GTDB sequences

*.${db}.gz

`names`

`meta`
`:map`

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

`${prefix}/*.names.dmp`
`:file`

NCBI taxonomy-style names.dmp text file

*.names.dmp

`nodes`

`meta`
`:map`

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

`${prefix}/*.nodes.dmp`
`:file`

NCBI taxonomy-style nodes.dmp text file

*.nodes.dmp

`acc2tax`

`meta`
`:map`

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

`${prefix}/accession2taxid.gz`
`:file`

NCBI taxonomy names accession to taxonomy file

*accession2taxid*

`log`

`meta`
`:map`

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

`${prefix}/*.log`
`:file`

Log file of the download process

*.log

`versions_catpack`

`${task.process}`
`:string`

The process the versions were collected from

`catpack`
`:string`

The tool name

`CAT_pack --version | sed 's/CAT_pack pack v//g;s/ .*//g'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`catpack`
`:string`

The name of the tool

`CAT_pack --version | sed 's/CAT_pack pack v//g;s/ .*//g'`
`: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

modules/catpack_download

Description

Input

`meta`
`:map`

`db`
`:string`

Output

`fasta`

`meta`
`:map`

`${prefix}/*.${db}.gz`
`:file`

`names`

`meta`
`:map`

`${prefix}/*.names.dmp`
`:file`

`nodes`

`meta`
`:map`

`${prefix}/*.nodes.dmp`
`:file`

`acc2tax`

`meta`
`:map`

`${prefix}/accession2taxid.gz`
`:file`

`log`

`meta`
`:map`

`${prefix}/*.log`
`:file`

`versions_catpack`

`${task.process}`
`:string`

`catpack`
`:string`

`CAT_pack --version | sed 's/CAT_pack pack v//g;s/ .*//g'`
`:eval`

Topics

`versions`

`${task.process}`
`:string`

`catpack`
`:string`

`CAT_pack --version | sed 's/CAT_pack pack v//g;s/ .*//g'`
`:eval`

Tools

catpack
MIT

included in

maintainer

get in touch

modules/catpack_download

Description

Input

meta:map

db:string

Output

fasta

meta:map

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

names

meta:map

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

nodes

meta:map

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

acc2tax

meta:map

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

log

meta:map

${prefix}/*.log:file

versions_catpack

${task.process}:string

catpack:string

CAT_pack --version | sed 's/CAT_pack pack v//g;s/ .*//g':eval

Topics

versions

${task.process}:string

catpack:string

CAT_pack --version | sed 's/CAT_pack pack v//g;s/ .*//g':eval

Tools

catpack MIT

included in

maintainer

get in touch

`meta`
`:map`

`db`
`:string`

`fasta`

`meta`
`:map`

`${prefix}/*.${db}.gz`
`:file`

`names`

`meta`
`:map`

`${prefix}/*.names.dmp`
`:file`

`nodes`

`meta`
`:map`

`${prefix}/*.nodes.dmp`
`:file`

`acc2tax`

`meta`
`:map`

`${prefix}/accession2taxid.gz`
`:file`

`log`

`meta`
`:map`

`${prefix}/*.log`
`:file`

`versions_catpack`

`${task.process}`
`:string`

`catpack`
`:string`

`CAT_pack --version | sed 's/CAT_pack pack v//g;s/ .*//g'`
`:eval`

`versions`

`${task.process}`
`:string`

`catpack`
`:string`

`CAT_pack --version | sed 's/CAT_pack pack v//g;s/ .*//g'`
`:eval`

catpack
MIT