modules/bracken_build

Extends a Kraken2 database to be compatible with Bracken

kraken2brackendatabasebuild

https://github.com/nf-core/modules/[...]/modules/nf-core/bracken/build

Description

Extends a Kraken2 database to be compatible with Bracken

Input

name:type

description

pattern

`meta`
`:map`

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

`k2d`
`:file`

Kraken2 k2d binary database files

*.k2d

`map`
`:file`

Kraken2 k2d binary database taxonomy to sequencing mapping file

*.map

`library`
`:file`

Kraken2 masked FASTA files used to build the database

*.fasta

`taxonomy`
`:file`

Kraken2 nodes.dmp, names.dmp, and .accession2taxid taxonomy files

*.{dmp,accession2taxid}

Output

name:type

description

pattern

`db`

`meta`
`:map`

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

`bracken-database/`
`:directory`

Directory contains the database that can be used to perform taxonomic classification

IMPORTANT: this output directory will be hardcoded as ‘bracken-database/’ inside the module to prevent issues of containers following symlinks in symlinks.

To give a user the option to provide custom name for the database directory within a pipeline, you should customise this name using during pipeline output publication via the pipeline’s publishDir or workflow output customisation options.

bracken-database/

`db_separated`

`meta`
`:map`

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

`bracken-database/database*`
`:file`

Bracken kmer distribution files

database*

`bracken-database/*k2d`
`:file`

Kraken2 k2d binary database files

*.k2d

`bracken-database/*map`
`:file`

Kraken2 k2d binary database taxonomy to sequencing mapping file

*.map

`bracken-database/library/added/*`
`:file`

Kraken2 masked FASTA files used to build the database

*.fasta

`bracken-database/taxonomy/*`
`:file`

Kraken2 nodes.dmp, names.dmp, and .accession2taxid taxonomy files

*.{dmp,accession2taxid}

`versions`

`versions.yml`
`:file`

File containing software versions

versions.yml

Tools

bracken
GPL v3

Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.

ccb.jhu.edu/software/bracken https://github.com/jenniferlu717/Bracken/ 10.7717/peerj-cs.104

modules/bracken_build

Description

Input

`meta`
`:map`

`k2d`
`:file`

`map`
`:file`

`library`
`:file`

`taxonomy`
`:file`

Output

`db`

`meta`
`:map`

`bracken-database/`
`:directory`

`db_separated`

`meta`
`:map`

`bracken-database/database*`
`:file`

`bracken-database/*k2d`
`:file`

`bracken-database/*map`
`:file`

`bracken-database/library/added/*`
`:file`

`bracken-database/taxonomy/*`
`:file`

`versions`

`versions.yml`
`:file`

Tools

bracken
GPL v3

included in

maintainer

get in touch

modules/bracken_build

Description

Input

meta:map

k2d:file

map:file

library:file

taxonomy:file

Output

db

meta:map

bracken-database/:directory

db_separated

meta:map

bracken-database/database*:file

bracken-database/*k2d:file

bracken-database/*map:file

bracken-database/library/added/*:file

bracken-database/taxonomy/*:file

versions

versions.yml:file

Tools

bracken GPL v3

included in

maintainer

get in touch

`meta`
`:map`

`k2d`
`:file`

`map`
`:file`

`library`
`:file`

`taxonomy`
`:file`

`db`

`meta`
`:map`

`bracken-database/`
`:directory`

`db_separated`

`meta`
`:map`

`bracken-database/database*`
`:file`

`bracken-database/*k2d`
`:file`

`bracken-database/*map`
`:file`

`bracken-database/library/added/*`
`:file`

`bracken-database/taxonomy/*`
`:file`

`versions`

`versions.yml`
`:file`

bracken
GPL v3