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

nf-core/irescue @ 0.0.0-0c7146d

Quantification of transposable elements expression in scRNA-seq

scRNA-seq transposons repeats

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @bepoli

Maintainers: @bepoli

Quantification of transposable elements expression in scRNA-seq

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

include { IRESCUE } from 'nf-core/irescue'

MIT License

Process

`Name`	`IRESCUE`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`bam` file	Sorted BAM file `*.bam`

`genome` string	Genome assembly symbol. Not used when bed file is provided. In this case, it can be any value or an empty string.

`bed` file	Bed file of repeats genomic coordinates (optional). `*.bed`

Output 5 channels

#1 log tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`${prefix}/irescue.log` file	Text file containing run information `${prefix}/irescue.log`

#2 tmp tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`${prefix}/tmp` directory	Folder containing temporary files, if kept using the "--keeptmp" argument (optional). `${prefix}/tmp`

#3 counts tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`${prefix}/counts` directory	Folder containing count matrices `${prefix}/counts`

#4 results tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`${prefix}` directory	Folder containing count matrices and logs `${prefix}`

#5 versions

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

Tool	Description	Homepage
irescue	IRescue is a tool for uncertainty-aware quantification of transposable elements expression in scRNA-seq	https://pypi.org/project/IRescue

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:49:25 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Firescue/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/irescue/blobs/sha256:30f0199617ff3eb1bf1f6a96822ada28f830a2ad186a676f1f0d0afc644c05e6
Size	2.7 KB
Checksum	sha256:30f0199617ff3eb1bf1f6a96822ada28f830a2ad186a676f1f0d0afc644c05e6
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:49:25 (UTC)		1	2.7 KB	-