modules/kraken2_build

Builds Kraken2 database

metagenomicsdbclassificationbuildkraken2

https://github.com/nf-core/modules/[...]/modules/nf-core/kraken2/build

Description

Builds Kraken2 database

Input

name:type

description

pattern

`meta`
`:map`

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

`library_added_files`
`:file`

Files present in the /library/added/ directory, including FASTA files, masked FASTAs, and prelim_map files.

*

`meta2`
`:map`

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

`seqid2taxid_map`
`:file`

File mapping sequence IDs to taxonomy IDs, either generated or premade.

seqid2taxid.map

`meta3`
`:map`

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

`taxonomy_files`
`:file`

Files present in the /taxonomy/ directory, including nodes.dmp, names.dmp, and .accession2taxid files.

*

`cleaning`
`:boolean`

activate or deactivate (true or false) cleaning of intermediate files

Output

name:type

description

pattern

`db`

`meta`
`:map`

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

`kraken2-database`
`:directory`

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

IMPORTANT: this output directory will be hardcoded as ‘kraken2-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.

kraken2-database/

`db_separated`

`meta`
`:map`

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

`kraken2-database/*k2d`
`:file`

Kraken2 k2d binary database files

*.k2d

`kraken2-database/*map`
`:file`

Kraken2 k2d binary database taxonomy to sequencing mapping file

*.map

`kraken2-database/library/added/*`
`:file`

Kraken2 masked FASTA files used to build the database

*.fasta

`kraken2-database/taxonomy/*`
`:file`

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

*.{dmp,accession2taxid}

`versions_kraken2`

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

The name of the process

`kraken2`
`:string`

The name of the tool

`kraken2 --version 2>&1 | head -1 | sed "s/^.Kraken version //; s/ .//"`
`:eval`

The expression to obtain the version of the tool

`unmapped`

`meta`
`:map`

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

`kraken2-database/unmapped*.txt`
`:file`

List of unmapped sequence files, i.e. accessions that did not map to any taxonomy ID and were excluded

unmapped*.txt

Topics

name:type

description

pattern

`versions`

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

The name of the process

`kraken2`
`:string`

The name of the tool

`kraken2 --version 2>&1 | head -1 | sed "s/^.Kraken version //; s/ .//"`
`:eval`

The expression to obtain the version of the tool

Tools

kraken2
MIT

Kraken2 is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.

args_id: $args

ccb.jhu.edu/software/kraken2 github.com/DerrickWood/kraken2/wiki/Manual https://github.com/DerrickWood/kraken2 10.1186/s13059-019-1891-0

modules/kraken2_build

Description

Input

`meta`
`:map`

`library_added_files`
`:file`

`meta2`
`:map`

`seqid2taxid_map`
`:file`

`meta3`
`:map`

`taxonomy_files`
`:file`

`cleaning`
`:boolean`

Output

`db`

`meta`
`:map`

`kraken2-database`
`:directory`

`db_separated`

`meta`
`:map`

`kraken2-database/*k2d`
`:file`

`kraken2-database/*map`
`:file`

`kraken2-database/library/added/*`
`:file`

`kraken2-database/taxonomy/*`
`:file`

`versions_kraken2`

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

`kraken2`
`:string`

`kraken2 --version 2>&1 | head -1 | sed "s/^.Kraken version //; s/ .//"`
`:eval`

`unmapped`

`meta`
`:map`

`kraken2-database/unmapped*.txt`
`:file`

Topics

`versions`

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

`kraken2`
`:string`

`kraken2 --version 2>&1 | head -1 | sed "s/^.Kraken version //; s/ .//"`
`:eval`

Tools

kraken2
MIT

included in

maintainers

get in touch

modules/kraken2_build

Description

Input

meta:map

library_added_files:file

meta2:map

seqid2taxid_map:file

meta3:map

taxonomy_files:file

cleaning:boolean

Output

db

meta:map

kraken2-database:directory

db_separated

meta:map

kraken2-database/*k2d:file

kraken2-database/*map:file

kraken2-database/library/added/*:file

kraken2-database/taxonomy/*:file

versions_kraken2

${task.process}:string

kraken2:string

kraken2 --version 2>&1 | head -1 | sed "s/^.*Kraken version //; s/ .*//":eval

unmapped

meta:map

kraken2-database/unmapped*.txt:file

Topics

versions

${task.process}:string

kraken2:string

kraken2 --version 2>&1 | head -1 | sed "s/^.*Kraken version //; s/ .*//":eval

Tools

kraken2 MIT

included in

maintainers

get in touch

`meta`
`:map`

`library_added_files`
`:file`

`meta2`
`:map`

`seqid2taxid_map`
`:file`

`meta3`
`:map`

`taxonomy_files`
`:file`

`cleaning`
`:boolean`

`db`

`meta`
`:map`

`kraken2-database`
`:directory`

`db_separated`

`meta`
`:map`

`kraken2-database/*k2d`
`:file`

`kraken2-database/*map`
`:file`

`kraken2-database/library/added/*`
`:file`

`kraken2-database/taxonomy/*`
`:file`

`versions_kraken2`

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

`kraken2`
`:string`

`kraken2 --version 2>&1 | head -1 | sed "s/^.Kraken version //; s/ .//"`
`:eval`

`unmapped`

`meta`
`:map`

`kraken2-database/unmapped*.txt`
`:file`

`versions`

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

`kraken2`
`:string`

`kraken2 --version 2>&1 | head -1 | sed "s/^.Kraken version //; s/ .//"`
`:eval`

kraken2
MIT