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nf-core/eggnogmapper @ 0.0.0-0c7146d

Fast genome-wide functional annotation through orthology assignment.

annotation functional annotation orthology genomics eggnog
Latest version: 0.0.0-0c7146d
Total downloads: 1
Source: nf-core/modules
Authors: @vagkaratzas
Maintainers: @vagkaratzas @gallvp

Summary

Fast genome-wide functional annotation through orthology assignment.

Get started

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

include { EGGNOGMAPPER } from 'nf-core/eggnogmapper'

License

MIT License

Process
Name EGGNOGMAPPER
Input 3 channels
#1 tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1' ]
fasta file

Input sequences in FASTA format (plain or gzip-compressed)

 *.{fasta,faa,fa}(.gz)?
#2 tuple
search_mode string

Search mode passed to emapper.py via -m. Determines which backend is used and which database flag is applied internally. Supported modes:

  • diamond: DIAMOND-based homology search (--dmnd_db)
  • novel_fams: DIAMOND search against novel families (--dmnd_db)
  • mmseqs: MMseqs2-based search (--mmseqs_db)
  • hmmer: HMMER-based search (--database)
  • no_search: Skip search step and annotate from a precomputed *.emapper.seed_orthologs file (--annotate_hits_table)
  • cache: Reuse a previously generated hits table (--cache)
db file

Database file, directory, or precomputed results file required by the selected search_mode. The module automatically assigns the correct flag depending on search_mode:

  • diamond / novel_fams: DIAMOND database (*.dmnd)
  • mmseqs: MMseqs2 database directory or prefix
  • hmmer: HMM database (*.hmm, *.h3m)
  • no_search: Precomputed *.emapper.seed_orthologs file
  • cache: Previously generated *.emapper.hits file This input is mandatory but its expected format depends on search_mode.
 *
eggnog_data_dir directory

Directory containing eggnog-mapper database files (e.g. can be downloaded via download_eggnog_data.py, found in the eggnog-mapper repository)

 *
Output 4 channels
#1 hits tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1' ]
*.emapper.hits file

TSV file with the raw search hits from the Diamond/MMseqs2/HMMER search phase before annotation

 *.emapper.hits
#2 orthologs tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1' ]
*.emapper.seed_orthologs file

TSV file with the results from parsing the hits, linking queries with their best seed orthologs (includes commented metadata header)

 *.emapper.seed_orthologs
#3 annotations tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1' ]
*.emapper.annotations file

TSV file with the results from the annotation phase, including functional annotations, GO terms, KEGG pathways, and COG categories

 *.emapper.annotations
#4 versions_eggnogmapper tuple
${task.process} string

The name of the process
eggnog-mapper string

The name of the tool
emapper.py --version 2>&1 | grep -o 'emapper-[0-9]\+\.[0-9]\+\.[0-9]\+' | sed 's/emapper-//' eval

The expression to obtain the version of the tool
Tool Description Homepage
eggnogmapper EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database to transfer functional information from fine-grained orthologs only. https://github.com/eggnogdb/eggnog-mapper
Version 0.0.0-0c7146d
Commit ID 135d883a43b1a2324b4112cd270cf22e20835533
Release Date 08 Apr 2026 18:36:43 (UTC)
Download URL https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Feggnogmapper/0.0.0-0c7146d/download
OCI Store URL https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/eggnogmapper/blobs/sha256:e9115fd278edf6f03aaa73274cdbf0cba1a23072ef84af5d648804e282b66606
Size 4.6 KB
Checksum sha256:e9115fd278edf6f03aaa73274cdbf0cba1a23072ef84af5d648804e282b66606
Downloads 1
Version Date Status Downloads Size Diff
0.0.0-0c7146d 08 Apr 2026 18:36:43 (UTC)