Nextflow Registry | nf-core/sortmerna@0.0.0-6c4ed3a

nf-core/sortmerna @ 0.0.0-6c4ed3a

Local sequence alignment tool for filtering, mapping and clustering.

filtering mapping clustering rRNA ribosomal RNA

Latest version: 0.0.0-6c4ed3a

Total downloads: 6

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	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:46:53 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fsortmerna/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/sortmerna/blobs/sha256:f3b7180715c4d5319c103c5a11faa359f5a360ca012acc91314a018b16314c57
Size	4.6 KB
Checksum	sha256:f3b7180715c4d5319c103c5a11faa359f5a360ca012acc91314a018b16314c57
Downloads	3

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:46:53 (UTC)		3	4.6 KB
0.0.0-0c7146d	08 Apr 2026 19:39:45 (UTC)