modules/kaiju_mergeoutputs

Merge two tab-separated output files of Kaiju and Kraken in the column format

classifymetagenomicsfastqtaxonomic profiling

https://github.com/nf-core/modules/[...]/modules/nf-core/kaiju/mergeoutputs

Description

Merge two tab-separated output files of Kaiju and Kraken in the column format

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`kaiju`
`:file`

Results with taxonomic classification of each read from Kaiju

`kraken`
`:file`

Results with taxonomic classification of each read from Kraken

*.{tsv}

`db`
`:directory`

List containing the database and nodes files for Kaiju e.g. [ ‘database.fmi’, ‘nodes.dmp’ ]

Output

name:type

description

pattern

`merged`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`*.tsv`
`:file`

Results with merged taxonomic classification of each read based on the given strategy ‘1’, ‘2’, ‘lca’ [default] or ‘lowest’

*.tsv

`versions_kaiju`

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

The name of the process

`kaiju`
`:string`

The name of the tool

`kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`kaiju`
`:string`

The name of the tool

`kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //'`
`:eval`

The expression to obtain the version of the tool

Tools

kaiju
GNU GPL v3

Fast and sensitive taxonomic classification for metagenomics

kaiju.binf.ku.dk github.com/bioinformatics-centre/kaiju/blob/master/README.md https://github.com/bioinformatics-centre/kaiju 10.1038/ncomms11257

modules/kaiju_mergeoutputs

Description

Input

`meta`
`:map`

`kaiju`
`:file`

`kraken`
`:file`

`db`
`:directory`

Output

`merged`

`meta`
`:map`

`*.tsv`
`:file`

`versions_kaiju`

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

`kaiju`
`:string`

`kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //'`
`:eval`

Topics

`versions`

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

`kaiju`
`:string`

`kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //'`
`:eval`

Tools

kaiju
GNU GPL v3

maintainer

get in touch

modules/kaiju_mergeoutputs

Description

Input

meta:map

kaiju:file

kraken:file

db:directory

Output

merged

meta:map

*.tsv:file

versions_kaiju

${task.process}:string

kaiju:string

kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //':eval

Topics

versions

${task.process}:string

kaiju:string

kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //':eval

Tools

kaiju GNU GPL v3

maintainer

get in touch

`meta`
`:map`

`kaiju`
`:file`

`kraken`
`:file`

`db`
`:directory`

`merged`

`meta`
`:map`

`*.tsv`
`:file`

`versions_kaiju`

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

`kaiju`
`:string`

`kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //'`
`:eval`

`versions`

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

`kaiju`
`:string`

`kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //'`
`:eval`

kaiju
GNU GPL v3