Nextflow Registry | nf-core/telescope/assign@0.0.0-6c4ed3a

nf-core/telescope/assign @ 0.0.0-6c4ed3a

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: 0.0.0-6c4ed3a

Total downloads: 3

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_bam` 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

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

#3 sam tuple

`meta_bam` 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_bam` 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	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:49:39 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Ftelescope%2Fassign/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/telescope/assign/blobs/sha256:b6ca843834027cd3a17e54bd34d6be682e7857acb4251675a86356932848e59c
Size	3.0 KB
Checksum	sha256:b6ca843834027cd3a17e54bd34d6be682e7857acb4251675a86356932848e59c
Downloads	2

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:49:39 (UTC)		2	3.0 KB
0.0.0-0c7146d	08 Apr 2026 19:43:27 (UTC)		1	3.0 KB