modules/catpack_bins

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/bins

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 ]

`bins`
`:file`

One or more nucleotide FASTA file containing binned long DNA sequences.

*.{fasta,fna,fa,fas}

`meta2`
`:map`

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

`database`
`:directory`

Directory containing CAT_pack database files (e.g. output from CAT_pack prepare)

*/

`meta3`
`:map`

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

`taxonomy`
`:directory`

Directory containing CAT_pack taxonomy files (e.g. output from CAT_pack prepare)

*/

`meta4`
`:map`

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

`proteins`
`:directory`

Optional pre predicted-made proteins FASTA

*.{fasta,faa,fa,fas}

`meta5`
`:map`

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

`diamond_table`
`:directory`

Optional pre-made DIAMOND alignment table

*

`bin_suffix`
`:string`

Suffix to search for in the input files when bins is a directory.

Output

name:type

description

pattern

`orf2lca`

`meta`
`:map`

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

`*.ORF2LCA.txt`
`:file`

A TSV file with per-ORF hit stats and identified lineage

*.ORF2LCA.txt

`bin2classification`

`meta`
`:map`

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

`*.bin2classification.txt`
`:file`

A TSV file with per-bin hit stats and assignment justification information

*.bin2classification.txt

`log`

`meta`
`:map`

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

`*.log`
`:file`

Log file with run messages and basic statistics

`diamond`

`meta`
`:map`

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

`*.diamond`
`:file`

Intermediate DIAMOND TSV summary output file with alignment results

`faa`

`meta`
`:map`

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

`*.predicted_proteins.faa`
`:file`

FAA file of DIAMOND predicted proteins hits

`gff`

`meta`
`:map`

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

`*.gff`
`:file`

GFF file of DIAMOND predicted proteins hits

`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_bins

Description

Input

meta:map

bins:file

meta2:map

database:directory

meta3:map

taxonomy:directory

meta4:map

proteins:directory

meta5:map

diamond_table:directory

bin_suffix:string

Output

orf2lca

meta:map

*.ORF2LCA.txt:file

bin2classification

meta:map

*.bin2classification.txt:file

log

meta:map

*.log:file

diamond

meta:map

*.diamond:file

faa

meta:map

*.predicted_proteins.faa:file

gff

meta:map

*.gff: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`

`bins`
`:file`

`meta2`
`:map`

`database`
`:directory`

`meta3`
`:map`

`taxonomy`
`:directory`

`meta4`
`:map`

`proteins`
`:directory`

`meta5`
`:map`

`diamond_table`
`:directory`

`bin_suffix`
`:string`

`orf2lca`

`meta`
`:map`

`*.ORF2LCA.txt`
`:file`

`bin2classification`

`meta`
`:map`

`*.bin2classification.txt`
`:file`

`log`

`meta`
`:map`

`*.log`
`:file`

`diamond`

`meta`
`:map`

`*.diamond`
`:file`

`faa`

`meta`
`:map`

`*.predicted_proteins.faa`
`:file`

`gff`

`meta`
`:map`

`*.gff`
`: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