Nextflow Registry | nf-core/htseq/count@0.0.0-0c7146d

nf-core/htseq/count @ 0.0.0-0c7146d

count how many reads map to each feature

htseq count gtf annotation

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @zehrahazalsezer

Maintainers: @zehrahazalsezer

count how many reads map to each feature

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

include { HTSEQ_COUNT } from 'nf-core/htseq/count'

MIT License

Process

`Name`	`HTSEQ_COUNT`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`input` file	Sorted BAM/CRAM/SAM file `*.{bam,cram,sam}`
`index` file	Contains indexed bam file `*.bai`

#2 tuple

`meta2` map	.gtf file information e.g. `[ id:'test' ]`
`gtf` file	Contains the features in the GTF format `*.gtf`

Output 2 channels

#1 txt tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`*.txt` file	File containing feature counts output `.txt`

#2 versions

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

Tool	Description	Homepage
htseq/count	HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.	https://htseq.readthedocs.io/en/latest/

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:48:23 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fhtseq%2Fcount/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/htseq/count/blobs/sha256:53de18d81b2ba723e69f63c2c7c8f0806bc75b234d4da91c0775eabe60df29a6
Size	2.4 KB
Checksum	sha256:53de18d81b2ba723e69f63c2c7c8f0806bc75b234d4da91c0775eabe60df29a6
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:48:23 (UTC)		1	2.4 KB	-