nf-core/bcftools/call @ 0.0.0-0c7146d
Summary
This command replaces the former bcftools view caller. Some of the original functionality has been temporarily lost in the process of transition under htslib, but will be added back on popular demand. The original calling model can be invoked with the -c option.
Get started
Add the following snippet to your workflow script to include this module.
include { BCFTOOLS_CALL } from 'nf-core/bcftools/call'
License
MIT License
Name
|
BCFTOOLS_CALL |
|---|
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
vcf
file
|
The vcf file to be inspected. e.g. 'file.vcf' |
index
file
|
The tab index for the VCF file to be inspected. e.g. 'file.tbi' |
regions
file
|
Optionally, restrict the operation to regions listed in this file. e.g. 'file.vcf' |
|---|
targets
file
|
Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files) e.g. 'file.vcf' |
|---|
samples
file
|
Optional, file of sample names to be included or excluded. e.g. 'file.tsv' |
|---|
csi
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.csi
file
|
Default VCF file index *.csi
|
tbi
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.tbi
file
|
Alternative VCF file index *.tbi
|
vcf
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.gz
file
|
VCF normalized output file *.{vcf.gz}
|
versions_bcftools
tuple
${task.process}
string
|
The process the versions were collected from |
|---|---|
bcftools
string
|
The tool name |
bcftools --version | sed '1!d; s/^.*bcftools //'
string
|
The command used to generate the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| view | View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF | http://samtools.github.io/bcftools/bcftools.html |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 18:24:59 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fbcftools%2Fcall/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/bcftools/call/blobs/sha256:e146cf5f7eac0d8466867c118b5d9199a0e3275817ee491ffe803ced17d365f4 |
| Size | 3.9 KB |
| Checksum | sha256:e146cf5f7eac0d8466867c118b5d9199a0e3275817ee491ffe803ced17d365f4 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 18:24:59 (UTC) | 1 | 3.9 KB | - |