nf-core/smncopynumbercaller @ 0.0.0-0c7146d
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 | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 19:15:04 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fsmncopynumbercaller/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/smncopynumbercaller/blobs/sha256:a0b778e6980dc9b1fea381802464d65b19a08466cb68d15888ee8d1c5b5212fc |
| Size | 2.6 KB |
| Checksum | sha256:a0b778e6980dc9b1fea381802464d65b19a08466cb68d15888ee8d1c5b5212fc |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 19:15:04 (UTC) | 1 | 2.6 KB | - |