Nextflow Registry | nf-core/sortmerna@0.0.0-0c7146d

nf-core/sortmerna @ 0.0.0-0c7146d

Local sequence alignment tool for filtering, mapping and clustering.

filtering mapping clustering rRNA ribosomal RNA

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @drpatelh @mashehu

Maintainers: @drpatelh @mashehu

Local sequence alignment tool for filtering, mapping and clustering.

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

include { SORTMERNA } from 'nf-core/sortmerna'

MIT License

Process

`Name`	`SORTMERNA`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`reads` file	List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.

#2 tuple

`meta2` map	Groovy Map containing reference information e.g. [ id:'test' ]
`fastas` file	Path to reference file(s)

#3 tuple

`meta3` map	Groovy Map containing index information e.g. [ id:'test' ]
`index` directory	Path to index directory of a previous sortmerna run

Output 4 channels

#1 log tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ], or reference information from an indexing-only run
`*.log` file	SortMeRNA log file `*sortmerna.log`

#2 index tuple

`meta2` map	Groovy Map containing reference information e.g. [ id:'test' ]
`idx` directory	Path to index directory generated by sortmern

#3 reads tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ], or reference information from an indexing-only run
`*non_rRNA.fastq.gz` file	The filtered fastq reads `*fastq.gz`

#4 versions_sortmerna tuple

`${task.process}` string	The process the versions were collected from
`sortmerna` string	The tool name
`sortmerna --version 2>&1 \| grep -oE "[0-9]+\.[0-9]+\.[0-9]+" \| head -1` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
SortMeRNA	The core algorithm is based on approximate seeds and allows for sensitive analysis of NGS reads. The main application of SortMeRNA is filtering rRNA from metatranscriptomic data. SortMeRNA takes as input files of reads (fasta, fastq, fasta.gz, fastq.gz) and one or multiple rRNA database file(s), and sorts apart aligned and rejected reads into two files. Additional applications include clustering and taxonomy assignation available through QIIME v1.9.1. SortMeRNA works with Illumina, Ion Torrent and PacBio data, and can produce SAM and BLAST-like alignments.	https://hpc.nih.gov/apps/sortmeRNA.html

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:15:42 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fsortmerna/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/sortmerna/blobs/sha256:fd6a94bf6b9714eaa5297d56dc45e71637e2ee8ded921ed9142588a65dae758f
Size	4.6 KB
Checksum	sha256:fd6a94bf6b9714eaa5297d56dc45e71637e2ee8ded921ed9142588a65dae758f
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:15:42 (UTC)		1	4.6 KB	-