Description

Fast genome-wide functional annotation through orthology assignment.

Input

name:type
description
pattern

meta{:bash}

:map

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

fasta{:bash}

:file

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

*.{fasta,faa,fa}(.gz)?

search_mode{:bash}

: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{:bash}

: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{:bash}

:directory

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

*

Output

name:type
description
pattern

annotations{:bash}

meta{:bash}

:map

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

*.emapper.annotations{:bash}

:file

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

*.emapper.annotations

orthologs{:bash}

meta{:bash}

:map

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

*.emapper.seed_orthologs{:bash}

:file

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

*.emapper.seed_orthologs

hits{:bash}

meta{:bash}

:map

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

*.emapper.hits{:bash}

:file

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

*.emapper.hits

versions_eggnogmapper{:bash}

${task.process}{:bash}

:string

The name of the process

eggnog-mapper{:bash}

:string

The name of the tool

emapper.py --version 2>&1 | grep -o 'emapper-[0-9]\+\.[0-9]\+\.[0-9]\+' | sed 's/emapper-//'{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

eggnog-mapper{:bash}

:string

The name of the tool

emapper.py --version 2>&1 | grep -o 'emapper-[0-9]\+\.[0-9]\+\.[0-9]\+' | sed 's/emapper-//'{:bash}

:eval

The expression to obtain the version of the tool

Tools

eggnogmapper
AGPL v3

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.

github.com/eggnogdb/eggnog-mapper github.com/eggnogdb/eggnog-mapper/wiki https://github.com/eggnogdb/eggnog-mapper 10.1093/molbev/msab293
maintainers
Github user vagkaratzas
Github user gallvp
get in touch
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