Description

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

Input

name:type
description
pattern

meta{:bash}

:map

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

input{:bash}

:file

Classification or ORF2LCA output file from CAT/BAT/RAT

*.txt

meta2{:bash}

:map

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

taxonomy{:bash}

:directory

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

*/

Output

name:type
description
pattern

txt{:bash}

meta{:bash}

:map

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

${prefix}.txt{:bash}

:map

CAT/BAT/RAT classification file with added taxonomic names

*.{bam,cram,sam}

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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