modules/gappa_examineassign

assigns taxonomy to query sequences in phylogenetic placement output

phylogenyphylogenetic placementclassificationtaxonomy

https://github.com/nf-core/modules/[...]/modules/nf-core/gappa/examineassign

Description

assigns taxonomy to query sequences in phylogenetic placement output

Input

name:type

description

pattern

`meta`
`:map`

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

`jplace`
`:file`

jplace file output from phylogenetic placement, e.g. EPA-NG, gzipped or not

*.{jplace,jplace.gz}

`taxonomy`
`:file`

taxonomy file

Output

name:type

description

pattern

`profile`

`meta`
`:map`

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

`*profile.tsv`
`:file`

profile tsv file

*profile.tsv

`labelled_tree`

`meta`
`:map`

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

`*labelled_tree.newick`
`:file`

labelled tree in newick format

*labelled_tree.newick

`per_query`

`meta`
`:map`

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

`*per_query.tsv`
`:file`

per query taxonomy assignments in tsv format

*per_query.tsv

`krona`

`meta`
`:map`

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

`*krona.profile`
`:file`

krona profile file

*krona.profile

`sativa`

`meta`
`:map`

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

`*sativa.tsv`
`:file`

sativa output file

*sativa.tsv

`versions_gappa`

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

The name of the process

`gappa`
`:string`

The name of the tool

`gappa --version 2>&1 | sed 's/v//'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`gappa`
`:string`

The name of the tool

`gappa --version 2>&1 | sed 's/v//'`
`:eval`

The expression to obtain the version of the tool

Tools

gappa
GPL v3

Genesis Applications for Phylogenetic Placement Analysis

github.com/lczech/gappa github.com/lczech/gappa/wiki https://github.com/lczech/gappa 10.1093/bioinformatics/btaa070

modules/gappa_examineassign

Description

Input

`meta`
`:map`

`jplace`
`:file`

`taxonomy`
`:file`

Output

`profile`

`meta`
`:map`

`*profile.tsv`
`:file`

`labelled_tree`

`meta`
`:map`

`*labelled_tree.newick`
`:file`

`per_query`

`meta`
`:map`

`*per_query.tsv`
`:file`

`krona`

`meta`
`:map`

`*krona.profile`
`:file`

`sativa`

`meta`
`:map`

`*sativa.tsv`
`:file`

`versions_gappa`

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

`gappa`
`:string`

`gappa --version 2>&1 | sed 's/v//'`
`:eval`

Topics

`versions`

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

`gappa`
`:string`

`gappa --version 2>&1 | sed 's/v//'`
`:eval`

Tools

gappa
GPL v3

included in

maintainer

get in touch

modules/gappa_examineassign

Description

Input

meta:map

jplace:file

taxonomy:file

Output

profile

meta:map

*profile.tsv:file

labelled_tree

meta:map

*labelled_tree.newick:file

per_query

meta:map

*per_query.tsv:file

krona

meta:map

*krona.profile:file

sativa

meta:map

*sativa.tsv:file

versions_gappa

${task.process}:string

gappa:string

gappa --version 2>&1 | sed 's/v//':eval

Topics

versions

${task.process}:string

gappa:string

gappa --version 2>&1 | sed 's/v//':eval

Tools

gappa GPL v3

included in

maintainer

get in touch

`meta`
`:map`

`jplace`
`:file`

`taxonomy`
`:file`

`profile`

`meta`
`:map`

`*profile.tsv`
`:file`

`labelled_tree`

`meta`
`:map`

`*labelled_tree.newick`
`:file`

`per_query`

`meta`
`:map`

`*per_query.tsv`
`:file`

`krona`

`meta`
`:map`

`*krona.profile`
`:file`

`sativa`

`meta`
`:map`

`*sativa.tsv`
`:file`

`versions_gappa`

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

`gappa`
`:string`

`gappa --version 2>&1 | sed 's/v//'`
`:eval`

`versions`

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

`gappa`
`:string`

`gappa --version 2>&1 | sed 's/v//'`
`:eval`

gappa
GPL v3