nf-core/pypgx/createinputvcf @ 0.0.0-0c7146d
Summary
Call SNVs/indels from BAM files for all target genes.
Get started
Add the following snippet to your workflow script to include this module.
include { PYPGX_CREATEINPUTVCF } from 'nf-core/pypgx/createinputvcf'
License
MIT License
Process
Name
|
PYPGX_CREATEINPUTVCF |
|---|
Input
2 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [id: 'test'] |
|---|---|
bam
file
|
Input BAM file *.{bam}
|
bai
file
|
Input BAM index file *.{bam.bai}
|
#2
tuple
meta2
map
|
Groovy Map containing sample information e.g. [id: 'test'] |
|---|---|
fasta
file
|
Reference genome file *.{fasta,fa,fna,fasta.gz,fa.gz,fna.gz}
|
Output
3 channels
#1
tbi
tuple
meta
map
|
Groovy Map containing sample information e.g. [id: 'test'] |
|---|---|
*.vcf.gz.tbi
file
|
File containing the VCF tabix index *.vcf.gz.tbi
|
#2
vcf
tuple
meta
map
|
Groovy Map containing sample information e.g. [id: 'test'] |
|---|---|
*.vcf.gz
file
|
VCF file containing called SNVs/indels *.vcf.gz
|
#3
versions_pypgx
tuple
${task.process}
string
|
The name of the process |
|---|---|
pypgx
string
|
The name of the tool |
pypgx -v 2>&1 | grep -oE "[0-9]+\.[0-9]+\.[0-9]+" | head -1
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| pypgx | A Python package for pharmacogenomics research | https://pypgx.readthedocs.io/en/latest/ |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 19:06:12 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fpypgx%2Fcreateinputvcf/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/pypgx/createinputvcf/blobs/sha256:79ab1b3f2f7c8bc6844b30dfa7dbddf6481bc8625b3cced90e8f32c3e02eba44 |
| Size | 2.7 KB |
| Checksum | sha256:79ab1b3f2f7c8bc6844b30dfa7dbddf6481bc8625b3cced90e8f32c3e02eba44 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 19:06:12 (UTC) | 1 | 2.7 KB | - |