nf-core/bcftools/stats @ 0.0.0-0c7146d
Summary
Generates stats from VCF files
Get started
Add the following snippet to your workflow script to include this module.
include { BCFTOOLS_STATS } from 'nf-core/bcftools/stats'
License
MIT License
Name
|
BCFTOOLS_STATS |
|---|
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
vcf
file
|
VCF input file *.{vcf}
|
tbi
file
|
The tab index for the VCF file to be inspected. Optional: only required when parameter regions is chosen. *.tbi
|
meta2
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
regions
file
|
Optionally, restrict the operation to regions listed in this file. (VCF, BED or tab-delimited) |
meta3
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
targets
file
|
Optionally, restrict the operation to regions listed in this file (doesn't rely upon tbi index files) |
meta4
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
samples
file
|
Optional, file of sample names to be included or excluded. e.g. 'file.tsv' |
meta5
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
exons
file
|
Tab-delimited file with exons for indel frameshifts (chr,beg,end; 1-based, inclusive, optionally bgzip compressed). e.g. 'exons.tsv.gz' |
meta6
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
fasta
file
|
Faidx indexed reference sequence file to determine INDEL context. e.g. 'reference.fa' |
stats
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*stats.txt
file
|
Text output file containing stats *_{stats.txt}
|
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 |
|---|---|---|
| stats | Parses VCF or BCF and produces text file stats which is suitable for machine processing and can be plotted using plot-vcfstats. | http://samtools.github.io/bcftools/bcftools.html |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 18:25:48 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fbcftools%2Fstats/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/bcftools/stats/blobs/sha256:9a9b6e96b85ae88af66bebb6e4c658e3ad644f748976bd5c90abf7ccdecd260f |
| Size | 3.4 KB |
| Checksum | sha256:9a9b6e96b85ae88af66bebb6e4c658e3ad644f748976bd5c90abf7ccdecd260f |