Nextflow Registry | nf-core/bcftools/pluginfixploidy@0.0.0-6c4ed3a

nf-core/bcftools/pluginfixploidy @ 0.0.0-6c4ed3a

The fixploidy plugin fixes ploidy in genotype fields according to specified ploidy rules, sample sex assignments, or a forced ploidy value. For example, haploid genotypes can be converted to diploid genotypes.

fixploidy bcftools ploidy vcf

Latest version: 0.0.0-6c4ed3a

Total downloads: 8

Source: nf-core/modules

Authors: @alkc

Maintainers: @alkc

Summary

Get started

Add the following snippet to your workflow script to include this module.

include { BCFTOOLS_PLUGINFIXPLOIDY } from 'nf-core/bcftools/pluginfixploidy'

License

MIT License

Process

`Name`	`BCFTOOLS_PLUGINFIXPLOIDY`

Input 5 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`vcf` file	Input VCF/BCF file to fix ploidy in. e.g. 'sample.vcf.gz'
`index` file	Index file for the input VCF/BCF (e.g. .tbi or .csi). e.g. 'sample.vcf.gz.tbi'

`ploidy` file	Optional ploidy definition file for the fixploidy plugin (`-p`), with space/tab-delimited columns: CHROM, FROM, TO, SEX, PLOIDY. e.g. 'ploidy.txt'

`sex` file	Optional sample sex assignment file for the fixploidy plugin (`-s`), containing lines of the form: NAME SEX. Samples not listed are treated as female by the plugin. e.g. 'samples_sex.txt'

`regions` file	Optionally restrict the operation to regions listed in this file (indexed input required; passed as a bcftools regions file argument). e.g. 'regions.bed'

`targets` file	Optionally restrict the operation to targets listed in this file (does not rely on index jumps in the same way as regions; passed as a bcftools targets file argument). e.g. 'targets.bed'

Output 4 channels

#1 csi tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.csi` file	Default VCF file index `*.csi`

#2 tbi tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.tbi` file	Alternative VCF file index `*.tbi`

#3 vcf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.{vcf,vcf.gz,bcf,bcf.gz}` file	VCF output file containing GT fields with modified ploidy `*.{vcf,vcf.gz,bcf,bcf.gz}`

#4 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 //'` eval	The command used to generate the version of the tool

Tool	Description	Homepage
bcftools	BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.	https://samtools.github.io/bcftools/howtos/index.html
bcftools plugin fixploidy	Bcftools plugins are tools that can be used with bcftools to manipulate variant calls in Variant Call Format (VCF) and BCF. The fixploidy plugin fixes ploidy in genotype fields according to specified ploidy rules, sample sex assignments, or a forced ploidy value. For example, haploid genotypes can be converted to diploid genotypes.	https://samtools.github.io/bcftools/howtos/plugins.html

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:05:06 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fbcftools%2Fpluginfixploidy/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/bcftools/pluginfixploidy/blobs/sha256:2783eea85492e376733bcc41abc6a006b7400f63b9b218c42a530d7556e7725e
Size	4.5 KB
Checksum	sha256:2783eea85492e376733bcc41abc6a006b7400f63b9b218c42a530d7556e7725e
Downloads	5