nf-core/subread/featurecounts @ 0.0.0-3fc6d40
Summary
Count reads that map to genomic features
Get started
Add the following snippet to your workflow script to include this module.
include { SUBREAD_FEATURECOUNTS } from 'nf-core/subread/featurecounts'
License
MIT License
Process
Name
|
SUBREAD_FEATURECOUNTS |
|---|
Input
1 channel
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
bams
file
|
BAM files containing mapped reads *.bam
|
annotation
file
|
Genomic features annotation in GTF or SAF *.{gtf,saf}
|
Output
3 channels
#1
counts
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*featureCounts.tsv
file
|
Counts of reads mapping to features *featureCounts.tsv
|
#2
summary
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*featureCounts.tsv.summary
file
|
Summary log file *.featureCounts.tsv.summary
|
#3
versions_subread
tuple
${task.process}
string
|
The name of the process |
|---|---|
subread
string
|
The name of the tool |
featureCounts -v 2>&1 | sed 's/featureCounts v//'
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| featurecounts | featureCounts is a highly efficient general-purpose read summarization program that counts mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations. It can be used to count both RNA-seq and genomic DNA-seq reads. | http://bioinf.wehi.edu.au/featureCounts/ |
| Version | 0.0.0-3fc6d40 |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 22 Apr 2026 15:32:56 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fsubread%2Ffeaturecounts/0.0.0-3fc6d40/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/subread/featurecounts/blobs/sha256:6020fe4c4b311c2b01e20ff2dcd4f6c7d0045815d1a7c894fcf14cc370a8ed59 |
| Size | 3.2 KB |
| Checksum | sha256:6020fe4c4b311c2b01e20ff2dcd4f6c7d0045815d1a7c894fcf14cc370a8ed59 |
| Downloads | 2 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:47:48 (UTC) | 3 | 3.2 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:32:56 (UTC) | 2 | 3.2 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:41:12 (UTC) | 3 | 3.2 KB |