Nextflow Registry | nf-core/mirdeep2/mapper@0.0.0-0c7146d

nf-core/mirdeep2/mapper @ 0.0.0-0c7146d

miRDeep2 Mapper is a tool that prepares deep sequencing reads for downstream miRNA detection by collapsing reads, mapping them to a genome, and outputting the required files for miRNA discovery.

mirdeep2 mapper RNA sequencing

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @atrigila

Maintainers: @atrigila

Summary

miRDeep2 Mapper is a tool that prepares deep sequencing reads for downstream miRNA detection by collapsing reads, mapping them to a genome, and outputting the required files for miRNA discovery.

Get started

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

include { MIRDEEP2_MAPPER } from 'nf-core/mirdeep2/mapper'

License

MIT License

Process

`Name`	`MIRDEEP2_MAPPER`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information, e.g. `[ id:'sample1', single_end:false ]`
`reads` file	File containing the raw sequencing reads that need to be collapsed and mapped to a reference genome. `*.fa`

#2 tuple

`meta2` map	Groovy Map containing information about the genome index.
`index` file	Path to the genome index file used for mapping the reads to the genome. `*`

Output 2 channels

#1 outputs tuple

`meta` map	Groovy Map containing sample information, e.g. `[ id:'sample1', single_end:false ]`
`*.fa` file	Collapsed reads in FASTA format. `*.fa`
`*.arf` file	Alignment Read Format (ARF) file containing the mapping of reads to the genome. `*.arf`

#2 versions

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

Tool	Description	Homepage
mirdeep2	miRDeep2 Mapper (`mapper.pl`) is part of the miRDeep2 suite. It collapses identical reads, maps them to a reference genome, and outputs both collapsed FASTA and ARF files for downstream miRNA detection and analysis.	https://www.mdc-berlin.de/content/mirdeep2-documentation

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:56:01 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fmirdeep2%2Fmapper/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/mirdeep2/mapper/blobs/sha256:cbb4e531786436bd2358d8fe4cc7ded03748b3ef12862104a6d459f168c59480
Size	3.2 KB
Checksum	sha256:cbb4e531786436bd2358d8fe4cc7ded03748b3ef12862104a6d459f168c59480
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:56:01 (UTC)		1	3.2 KB	-