nf-core/cnvpytor/importreaddepth @ 0.0.0-0c7146d
Summary
command line tool for CNV/CNA analysis. This step imports the read depth data into a root pytor file.
Get started
Add the following snippet to your workflow script to include this module.
include { CNVPYTOR_IMPORTREADDEPTH } from 'nf-core/cnvpytor/importreaddepth'
License
MIT License
Process
Name
|
CNVPYTOR_IMPORTREADDEPTH |
|---|
Input
2 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test' ] |
|---|---|
input_file
file
|
BAM/CRAM/SAM file *.{bam,cram}
|
index
file
|
bam file index *.{bai,crai}
|
#2
tuple
meta2
map
|
Groovy Map containing genome information e.g. [ id:'genome' ] |
|---|---|
fasta
file
|
specifies reference genome file (only for cram file without reference genome) *.{fasta,fasta.gz,fa,fa.gz}
|
fai
file
|
Index of reference fasta file *.fai
|
Output
2 channels
#1
pytor
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test' ] |
|---|---|
*.pytor
file
|
read depth root file in which read depth data binned to 100 base pair bins will be stored. *.{pytor}
|
#2
versions_cnvpytor
tuple
${task.process}
string
|
The name of the process |
|---|---|
cnvpytor
string
|
The name of the tool |
cnvpytor --version 2>&1 | sed -n 's/.*CNVpytor //p'
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| cnvpytor -rd | calling CNVs using read depth | https://github.com/abyzovlab/CNVpytor |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 18:32:02 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fcnvpytor%2Fimportreaddepth/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/cnvpytor/importreaddepth/blobs/sha256:010d59a5daedc2b3d6d217843c3871e4211c1399ef6aaf632ec52c8b0777e2ff |
| Size | 2.7 KB |
| Checksum | sha256:010d59a5daedc2b3d6d217843c3871e4211c1399ef6aaf632ec52c8b0777e2ff |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 18:32:02 (UTC) | 1 | 2.7 KB | - |