modules/catpack_addnames

Taxonomic classification of long DNA sequences and metagenome assembled genomes (e.g. MAGs / bins).

taxonomic classificationclassificationlong readsmagsassembly

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

Description

Taxonomic classification of long DNA sequences and metagenome assembled genomes (e.g. MAGs / bins).

Input

name:type

description

pattern

`meta`
`:map`

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

`input`
`:file`

Classification or ORF2LCA output file from CAT/BAT/RAT

*.txt

`meta2`
`:map`

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

`taxonomy`
`:directory`

Directory containing taxonomy files: names.dmp, nodes.dmp, acc2taxid.txt

*/

Output

name:type

description

pattern

`txt`

`meta`
`:map`

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

`${prefix}.txt`
`:map`

CAT/BAT/RAT classification file with added taxonomic names

*.{bam,cram,sam}

`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_addnames

Description

Input

`meta`
`:map`

`input`
`:file`

`meta2`
`:map`

`taxonomy`
`:directory`

Output

`txt`

`meta`
`:map`

`${prefix}.txt`
`:map`

`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_addnames

Description

Input

meta:map

input:file

meta2:map

taxonomy:directory

Output

txt

meta:map

${prefix}.txt:map

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`

`input`
`:file`

`meta2`
`:map`

`taxonomy`
`:directory`

`txt`

`meta`
`:map`

`${prefix}.txt`
`:map`

`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