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nf-core/ribodetector @ 0.0.0-3fc6d40

Accurate and rapid RiboRNA sequences Detector based on deep learning

RNA RNAseq rRNA ribosomal RNA rRNA depletion rRNA removal rRNA filtering deep learning Riboseq genomics
Latest version: 0.0.0-6c4ed3a
Total downloads: 15
Source: nf-core/modules
Authors: @maxibor
Maintainers: @maxibor

Summary

Accurate and rapid RiboRNA sequences Detector based on deep learning

Get started

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

include { RIBODETECTOR } from 'nf-core/ribodetector'

License

MIT License

Process
Name RIBODETECTOR
Input 2 channels
#1 tuple
meta map

Groovy Map containing riboseq sample information e.g. `[ id:'sample1', single_end:false ]
fastq file

List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.
length integer

Sequencing read length (mean length). Note: the accuracy reduces for reads shorter than 40

 integer >= 1
Output 4 channels
#1 log tuple
meta map

Groovy Map containing sample information
*.log file

Log file from RiboDetector

 *.log
#2 fastq tuple
meta map

Groovy Map containing sample information
*.nonrna*.fastq.gz file

rRNA depleted FastQ files

 *.nonrna*.fastq.gz
#3 versions_cuda tuple
${task.process} string

Name of the process
cuda string

Name of the runtime
python -c "import torch; print(torch.version.cuda or 'no CUDA available')" eval

CUDA version bundled with the task's pytorch build, or no CUDA available on the non-GPU path
#4 versions_ribodetector tuple
${task.process} string

Name of the process
ribodetector string

Name of the tool
ribodetector --version | sed "s/ribodetector //" eval

The expression to obtain the version of the tool
Tool Description Homepage
ribodetector Accurate and rapid RiboRNA sequences detector based on deep learning. RiboDetector uses a deep learning approach to identify rRNA sequences in ribosome profiling (Ribo-seq) data. It can be used to filter out rRNA reads from Ribo-seq datasets, improving the quality of downstream analyses. As of version 0.3.1, Ribodetector doesn't support setting a random seed, so results may not be fully deterministic across runs. https://github.com/hzi-bifo/RiboDetector
Version 0.0.0-3fc6d40
Commit ID 6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date 22 Apr 2026 15:29:00 (UTC)
Download URL https://registry.nextflow.io/api/v1/modules/nf-core%2Fribodetector/0.0.0-3fc6d40/download
OCI Store URL https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/ribodetector/blobs/sha256:e35f14f257ea8186da971e0e1455607f587f8bb5f89348e038fb4747e893ce6f
Size 82.7 KB
Checksum sha256:e35f14f257ea8186da971e0e1455607f587f8bb5f89348e038fb4747e893ce6f
Downloads 4
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Version Date Status Downloads Size
0.0.0-6c4ed3a 23 Apr 2026 15:40:55 (UTC) 3 82.7 KB
0.0.0-3fc6d40 22 Apr 2026 15:29:00 (UTC) 4 82.7 KB
0.0.0-7f68141 16 Apr 2026 15:01:17 (UTC) 4 82.7 KB
0.0.0-20423f5 14 Apr 2026 15:00:18 (UTC)