nf-core/pypgx/createinputvcf @ 0.0.0-6c4ed3a
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 | 0.0.0-6c4ed3a |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 23 Apr 2026 15:39:08 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fpypgx%2Fcreateinputvcf/0.0.0-6c4ed3a/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/pypgx/createinputvcf/blobs/sha256:06ba7b8290630529a360d8edbc1c127cf7b523bc087f238b9f5da05d7fb45543 |
| Size | 2.7 KB |
| Checksum | sha256:06ba7b8290630529a360d8edbc1c127cf7b523bc087f238b9f5da05d7fb45543 |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:39:08 (UTC) | 3 | 2.7 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:27:58 (UTC) | 3 | 2.8 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:29:30 (UTC) | 3 | 2.7 KB |