nf-core/bamreadcount @ 0.0.0-6c4ed3a
Summary
bam-readcount is a utility that runs on a BAM or CRAM file and generates low-level information about sequencing data at specific nucleotide positions. Its outputs include observed bases, readcounts, summarized mapping and base qualities, strandedness information, mismatch counts, and position within the reads.
Get started
Add the following snippet to your workflow script to include this module.
include { BAMREADCOUNT } from 'nf-core/bamreadcount'
License
MIT License
Process
Name
|
BAMREADCOUNT |
|---|
Input
3 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
bam
file
|
Sorted BAM/CRAM file *.{bam,cram}
|
bai
file
|
BAM/CRAM index file *.{bai,crai}
|
reference
file
|
Reference genome FASTA file *.{fa,fasta,fa.gz,fasta.gz}
|
|---|
bed
file
|
BED file with regions to analyze *.bed
|
|---|
Output
2 channels
#1
rc
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
*.rc
file
|
Readcount file with metrics *.rc
|
#2
versions_bamreadcount
tuple
${task.process}
string
|
The name of the process |
|---|---|
bamreadcount
string
|
The name of the tool |
bam-readcount --version | awk -F'version: ' '{print \$2}' | awk -F'-' '{print \$1}'
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| bamreadcount | bam-readcount generates metrics at single nucleotide positions. | https://github.com/genome/bam-readcount/blob/master/README.md |
| Version | 0.0.0-6c4ed3a |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 23 Apr 2026 15:03:21 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fbamreadcount/0.0.0-6c4ed3a/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/bamreadcount/blobs/sha256:eec2ff716d013e2ec4bd31cd3764f89ffefe1095f1985ec77718904c60f78c85 |
| Size | 2.6 KB |
| Checksum | sha256:eec2ff716d013e2ec4bd31cd3764f89ffefe1095f1985ec77718904c60f78c85 |
| Downloads | 4 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:03:21 (UTC) | 4 | 2.6 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:02:38 (UTC) | 3 | 2.6 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 18:44:14 (UTC) | 3 | 2.6 KB |