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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: 0.0.0-6c4ed3a
Total downloads: 11
Source: nf-core/modules
Authors: @vagkaratzas
Maintainers: @vagkaratzas

Summary

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

Get started

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

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

License

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 6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date 08 Apr 2026 19:09:49 (UTC)
Download URL https://registry.nextflow.io/api/v1/modules/nf-core%2Fhmmer%2Fjackhmmer/0.0.0-0c7146d/download
OCI Store URL https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/hmmer/jackhmmer/blobs/sha256:dc72fae6b5c2d9a253b059356488dabc246dbbe510bea40f8d070835bc086eff
Size 3.1 KB
Checksum sha256:dc72fae6b5c2d9a253b059356488dabc246dbbe510bea40f8d070835bc086eff
Downloads 4
Version Date Status Downloads Size
0.0.0-6c4ed3a 23 Apr 2026 15:24:27 (UTC) 4 3.1 KB
0.0.0-3fc6d40 22 Apr 2026 15:16:36 (UTC) 3 3.1 KB
0.0.0-0c7146d 08 Apr 2026 19:09:49 (UTC) 4 3.1 KB
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