Nextflow Registry | nf-core/telescope/assign@0.0.0-e2d3f0d

nf-core/telescope/assign @ 0.0.0-e2d3f0d

The telescope assign program finds overlapping reads between an alignment (SAM/BAM) and an annotation (GTF) then reassigns reads using a statistical model.

EM single-locus transcriptomics

Latest version: 0.0.0-e2d3f0d

Total downloads: 2

Source: nf-core/modules

Authors: @hanalysis

Maintainers: @hanalysis

Summary

The telescope assign program finds overlapping reads between an alignment (SAM/BAM) and an annotation (GTF) then reassigns reads using a statistical model.

Get started

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

include { TELESCOPE_ASSIGN } from 'nf-core/telescope/assign'

License

MIT License

Process

`Name`	`TELESCOPE_ASSIGN`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`bam` file	Sorted BAM/CRAM/SAM file, File must be collated so that all alignments for a read pair appear sequentially in the file `*.{bam,sam}`

#2 tuple

`meta2` map	Groovy Map containing sample information e.g. `[id:'sample1' ]`
`gtf` file	Annotation file which includes TE loci. `*.{gtf}`

Output 5 channels

#1 bam tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*{updated,other}.bam` file	The updated SAM file contains those fragments that has at least 1 initial alignment to a transposable element. `*{updated,other}.bam`

#2 log tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*.log` file	Log file for telescope run output. `*.log`

#3 sam tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*{updated,other}.sam` file	The updated SAM file contains those fragments that has at least 1 initial alignment to a transposable element. `*{updated,other}.bam`

#4 tsv tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*.tsv` file	Statistical report associated with the run `*.tsv`

#5 versions_telescope tuple

`${task.process}` string	The process the versions were collected from
`telescope` string	The tool name
`telescope --version \| sed '1!d;s/.* //'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
telescope	Single locus resolution of Transposable ELEment expression	https://github.com/mlbendall/telescope

Version	0.0.0-e2d3f0d
Commit ID	e2d3f0ddf4a74a4a9031f3caea2e9deaec5a440b
Release Date	28 Apr 2026 21:15:59 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Ftelescope%2Fassign/0.0.0-e2d3f0d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/telescope/assign/blobs/sha256:db29716a31a5e1141ca78298b09d8cb81ac307ae63b4bf6eca3479421ecb98cd
Size	3.1 KB
Checksum	sha256:db29716a31a5e1141ca78298b09d8cb81ac307ae63b4bf6eca3479421ecb98cd
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-e2d3f0d	28 Apr 2026 21:15:59 (UTC)		1	3.1 KB	↔
0.0.0-0c7146d	08 Apr 2026 19:19:16 (UTC)		1