Nextflow Registry | nf-core/gappa/examineassign@0.0.0-0c7146d

nf-core/gappa/examineassign @ 0.0.0-0c7146d

assigns taxonomy to query sequences in phylogenetic placement output

phylogeny phylogenetic placement classification taxonomy

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @erikrikarddaniel

Maintainers: @erikrikarddaniel

assigns taxonomy to query sequences in phylogenetic placement output

Add the following snippet to your workflow script to include this module.

include { GAPPA_EXAMINEASSIGN } from 'nf-core/gappa/examineassign'

MIT License

Process

`Name`	`GAPPA_EXAMINEASSIGN`

Input 1 channel

#1 tuple

`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 7 channels

#1 krona tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*krona.profile` file	krona profile file `*krona.profile`

#2 sativa tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*sativa.tsv` file	sativa output file `*sativa.tsv`

#3 profile tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*profile.tsv` file	profile tsv file `*profile.tsv`

#4 versions

`versions.yml` file	File containing software versions `versions.yml`

#5 per_query tuple

`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`

#6 examineassign tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`./.` directory	Execution directory

#7 labelled_tree tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*labelled_tree.newick` file	labelled tree in newick format `*labelled_tree.newick`

Tool	Description	Homepage
gappa	Genesis Applications for Phylogenetic Placement Analysis	https://github.com/lczech/gappa

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:40:41 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fgappa%2Fexamineassign/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/gappa/examineassign/blobs/sha256:dd296fca0e6a98398a84a52ee0b3c72270a50963623d2a03dc9db49db1396cc8
Size	2.7 KB
Checksum	sha256:dd296fca0e6a98398a84a52ee0b3c72270a50963623d2a03dc9db49db1396cc8
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:40:41 (UTC)		1	2.7 KB	-