nf-core/htseq/count @ 0.0.0-6c4ed3a
Summary
count how many reads map to each feature
Get started
Add the following snippet to your workflow script to include this module.
include { HTSEQ_COUNT } from 'nf-core/htseq/count'
License
MIT License
Process
Name
|
HTSEQ_COUNT |
|---|
Input
2 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
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. |
|---|---|
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. |
|---|---|
*.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 | 0.0.0-6c4ed3a |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 23 Apr 2026 15:24:42 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fhtseq%2Fcount/0.0.0-6c4ed3a/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/htseq/count/blobs/sha256:29575ed528eb0e4ed428e819c6c5358c6c1a9cff8b647946839d52fcd55966a1 |
| Size | 2.4 KB |
| Checksum | sha256:29575ed528eb0e4ed428e819c6c5358c6c1a9cff8b647946839d52fcd55966a1 |
| Downloads | 4 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:24:42 (UTC) | 4 | 2.4 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:16:40 (UTC) | 3 | 2.4 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:10:11 (UTC) | 3 | 2.4 KB |