nf-core/smncopynumbercaller @ 0.0.0-6c4ed3a
Summary
tool to call the copy number of full-length SMN1, full-length SMN2, as well as SMN2Δ7–8 (SMN2 with a deletion of Exon7-8) from a whole-genome sequencing (WGS) BAM file.
Get started
Add the following snippet to your workflow script to include this module.
include { SMNCOPYNUMBERCALLER } from 'nf-core/smncopynumbercaller'
License
MIT License
Process
Name
|
SMNCOPYNUMBERCALLER |
|---|
Input
1 channel
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
bam
file
|
BAM/CRAM file *.{bam,cram}
|
bai
file
|
BAM/CRAM index file *.{bai,crai}
|
Output
3 channels
#1
run_metrics
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
out/*.json
file
|
File containing run parameters of SMNCopyNumberCaller *.{json}
|
#2
smncopynumber
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
out/*.tsv
file
|
File containing the output of SMNCopyNumberCaller *.{tsv}
|
#3
versions_smncopynumbercaller
tuple
${task.process}
string
|
The name of the process |
|---|---|
smncopynumbercaller
string
|
The name of the tool |
1.1.2
string
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| smncopynumbercaller | call copy number of SMN1, SMN2, SMN2Δ7–8 from a bam file | https://github.com/Illumina/SMNCopyNumberCaller |
| Version | 0.0.0-6c4ed3a |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 23 Apr 2026 15:46:28 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fsmncopynumbercaller/0.0.0-6c4ed3a/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/smncopynumbercaller/blobs/sha256:3b0c55b76c3a69c3887e6f6974a90276feb1d972d25c5ab1de632e20610b0833 |
| Size | 2.6 KB |
| Checksum | sha256:3b0c55b76c3a69c3887e6f6974a90276feb1d972d25c5ab1de632e20610b0833 |
| Downloads | 4 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:46:28 (UTC) | 4 | 2.6 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:32:08 (UTC) | 3 | 2.6 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:39:07 (UTC) | 4 | 2.6 KB |