nf-core/cnvpytor/importreaddepth @ 0.0.0-5d5b444
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 | 0.0.0-5d5b444 |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 21 Apr 2026 15:00:49 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fcnvpytor%2Fimportreaddepth/0.0.0-5d5b444/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/cnvpytor/importreaddepth/blobs/sha256:6047d8a589c074f229c847833fa8dfc6944dedaa7607d10d47467c17c3836626 |
| Size | 2.6 KB |
| Checksum | sha256:6047d8a589c074f229c847833fa8dfc6944dedaa7607d10d47467c17c3836626 |
| Downloads | 2 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:10:51 (UTC) | 3 | 2.6 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:07:22 (UTC) | 3 | 2.6 KB | |
| 0.0.0-5d5b444 | 21 Apr 2026 15:00:49 (UTC) | 2 | 2.6 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 18:53:22 (UTC) | 4 | 2.7 KB |