modules/kaiju_kaiju2krona

Convert Kaiju’s tab-separated output file into a tab-separated text file which can be imported into Krona.

taxonomyvisualisationkrona chartmetagenomics

https://github.com/nf-core/modules/[...]/modules/nf-core/kaiju/kaiju2krona

Description

Convert Kaiju’s tab-separated output file into a tab-separated text file which can be imported into Krona.

Input

name:type

description

pattern

`meta`
`:map`

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

`tsv`
`:file`

Kaiju tab-separated output file

*.{tsv,txt}

`db`
`:file`

Kaiju database file

Output

name:type

description

pattern

`txt`

`meta`
`:map`

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

`*.txt`
`:file`

Krona text-based input file converted from Kaiju report

*.{txt,krona}

`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_kaiju2krona

Description

Input

`meta`
`:map`

`tsv`
`:file`

`db`
`:file`

Output

`txt`

`meta`
`:map`

`*.txt`
`: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

included in

maintainer

get in touch

modules/kaiju_kaiju2krona

Description

Input

meta:map

tsv:file

db:file

Output

txt

meta:map

*.txt: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

included in

maintainer

get in touch

`meta`
`:map`

`tsv`
`:file`

`db`
`:file`

`txt`

`meta`
`:map`

`*.txt`
`: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