Nextflow Registry | nf-core/hmmer/jackhmmer@0.0.0-0c7146d

nf-core/hmmer/jackhmmer @ 0.0.0-0c7146d

iterative searches to detect distant homologs by refining an HMM profile from hits

HMM homologs iterative model refinement

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @vagkaratzas

Maintainers: @vagkaratzas

iterative searches to detect distant homologs by refining an HMM profile from hits

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

include { HMMER_JACKHMMER } from 'nf-core/hmmer/jackhmmer'

MIT License

Process

`Name`	`HMMER_JACKHMMER`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`fasta` file	One or multiple amino acid sequences from which to start building a model iteratively (one model per input sequence) `*.{fasta,fna,faa,fa,fasta.gz,fna.gz,faa.gz,fa.gz}`
`seqdb` file	Database of sequences in FASTA format `*.{fasta,fna,faa,fa,fasta.gz,fna.gz,faa.gz,fa.gz}`
`write_align` boolean	Flag to save optional alignment output. Specify with 'true' to save.
`write_target` boolean	Flag to save optional per target summary. Specify with 'true' to save.
`write_domain` boolean	Flag to save optional per domain summary. Specify with 'true' to save.

Output 5 channels

#1 output tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.txt.gz` file	Human readable output summarizing hmmsearch results `*.{txt.gz}`

#2 versions

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

#3 alignments tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.sto.gz` file	Optional multiple sequence alignment (MSA) in Stockholm format `*.{sto.gz}`

#4 domain_summary tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.domtbl.gz` file	Optional tabular (space-delimited) summary of per-domain output `*.{domtbl.gz}`

#5 target_summary tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.tbl.gz` file	Optional tabular (space-delimited) summary of per-target output `*.{tbl.gz}`

Tool	Description	Homepage
hmmer	Biosequence analysis using profile hidden Markov models	http://hmmer.org/

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:48:02 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fhmmer%2Fjackhmmer/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/hmmer/jackhmmer/blobs/sha256:7c89cde6c0a216aa71ecf56b7423028002eafd631a376147bb7a7a0e2edf9d9a
Size	3.1 KB
Checksum	sha256:7c89cde6c0a216aa71ecf56b7423028002eafd631a376147bb7a7a0e2edf9d9a
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:48:02 (UTC)		1	3.1 KB	-