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

nf-core/tetranscripts @ 0.0.0-0c7146d

Runs TEtranscripts which summarises transposable element content of a bam file.

transposable TE transcriptomics

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @hanalysis

Maintainers: @hanalysis

Runs TEtranscripts which summarises transposable element content of a bam file.

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

include { TETRANSCRIPTS } from 'nf-core/tetranscripts'

MIT License

Process

`Name`	`TETRANSCRIPTS`

Input 4 channels

#1 tuple

`meta_t` map	Groovy Map containing treatment sample information. e.g. `[ id:'sample1' ]`
`bam_t` file	A BAM file for the treatment condition `*.{bam}`

#2 tuple

`meta_c` map	Groovy Map containing control sample information, e.g. `[ id:'control1']`
`bam_c` file	A BAM file for the control condition `*.{bam}`

#3 tuple

`meta_ggtf` map	Groovy map containing control sample information e.g. `[ id:'control1' ]`
`g_gtf` file	A GTF file for alignment to the genome `*.{gtf}`

#4 tuple

`meta_tegtf` map	Groovy map containing TE GTF information e.g. `[ id:'control1' ]`
`te_gtf` file	A curated GTF file for alignment to transposable elements `*.{gtf}`

Output 5 channels

#1 log2fc tuple

`meta_t` map	Groovy Map containing treatment sample information. e.g. `id:'sample1' ]`
`*.R` file	Differential gene expression analysis file `*.R`

#2 sigdiff tuple

`meta_t` map	Groovy map containing treatment sample information. e.g. `id:'sample1' ]`
`*_gene_TE.txt` file	DESeq2 analysis file `*_gene_TE.txt`

#3 analysis tuple

`meta_t` map	Groovy map containing treatment sample information. e.g. `id:'sample1' ]`
`*_analysis.txt` file	DESeq2 analysis file `*_analysis.txt`

#4 countTable tuple

`meta_t` map	Groovy Map containing treatment sample information. e.g. `id:'sample1' ]`
`*.cntTable` file	Counts table of transposable element families `*.cntTable`

#5 versions_tetranscripts tuple

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

Tool	Description	Homepage
tetranscripts	A package for including transposable elements in differential enrichment analysis of sequencing datasets.	https://github.com/mhammell-laboratory/TEtranscripts

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:19:24 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Ftetranscripts/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/tetranscripts/blobs/sha256:79f2e595dc80e1ac1ca4cc20cb6840fc199dfb24e67a6d2c96ec2c0949e97bcd
Size	3.5 KB