Nextflow Registry | nf-core/infernal/cmsearch@0.0.0-e2d3f0d

nf-core/infernal/cmsearch @ 0.0.0-e2d3f0d

Search covariance models against a sequence database

rrna covariance model sequence search

Latest version: 0.0.0-e2d3f0d

Total downloads: 2

Source: nf-core/modules

Authors: @prototaxites

Maintainers: @prototaxites

Search covariance models against a sequence database

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

include { INFERNAL_CMSEARCH } from 'nf-core/infernal/cmsearch'

MIT License

Process

`Name`	`INFERNAL_CMSEARCH`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`cmfile` file	A calibrated Infernal covariance model file
`seqdb` file	A FASTA file of sequences to search the covariance models against. Can be gzipped.

`write_align` boolean	Flag to save optional alignment output in Stockholm format. Specify with 'true' to save.

`write_target` boolean	Flag to save optional per target summary in a tabular format. Specify with 'true' to save.

Output 5 channels

#1 output tuple

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

#2 alignments tuple

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

#3 versions_gzip tuple

`${task.process}` string	The name of the process
`gzip` string	The name of the tool
`gzip --version \|& sed '1!d;s/gzip //'` eval	The expression to obtain the version of the tool

#4 target_summary tuple

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

#5 versions_infernal tuple

`${task.process}` string	The name of the process
`infernal` string	The name of the tool
`cmsearch -h \| sed '2!d;s/.INFERNAL //;s/ .//'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
infernal	Infernal is for searching DNA sequence databases for RNA structure and sequence similarities.	http://eddylab.org/infernal/Userguide.pdf

Version	0.0.0-e2d3f0d
Commit ID	e2d3f0ddf4a74a4a9031f3caea2e9deaec5a440b
Release Date	28 Apr 2026 21:15:43 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Finfernal%2Fcmsearch/0.0.0-e2d3f0d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/infernal/cmsearch/blobs/sha256:bd6e48ee2f34fc41967e12438f2a2ede21eae33ea31a68be80943f7b586deb68
Size	3.6 KB
Checksum	sha256:bd6e48ee2f34fc41967e12438f2a2ede21eae33ea31a68be80943f7b586deb68
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-e2d3f0d	28 Apr 2026 21:15:43 (UTC)		1	3.6 KB