Nextflow Registry | nf-core/gatk4/sitedepthtobaf@0.0.0-0c7146d

nf-core/gatk4/sitedepthtobaf @ 0.0.0-0c7146d

EXPERIMENTAL TOOL! Convert SiteDepth to BafEvidence

baf gatk4 site depth

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @nvnieuwk

Maintainers: @nvnieuwk

EXPERIMENTAL TOOL! Convert SiteDepth to BafEvidence

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

include { GATK4_SITEDEPTHTOBAF } from 'nf-core/gatk4/sitedepthtobaf'

MIT License

Process

`Name`	`GATK4_SITEDEPTHTOBAF`

Input 5 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`site_depths` file	Files containing site depths `*.sd.txt.gz`
`site_depths_indices` file	The indices of the site depth files `*.sd.txt.gz.tbi`

#2 tuple

`vcf` file	Input VCF of SNPs marking loci for site depths `*.vcf.gz`
`tbi` file	Index of the input VCF of SNPs marking loci for site depths `*.vcf.gz.tbi`

`fasta` file	The reference FASTA file `*.{fasta,fa}`

`fasta_fai` file	The index of the reference FASTA file `*.fai`

`dict` file	The sequence dictionary of the reference FASTA file `*.dict`

Output 3 channels

#1 baf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.baf.txt.gz` file	The created BAF file `*.baf.txt.gz`

#2 baf_tbi tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.baf.txt.gz.tbi` file	The index of the created BAF file `*.baf.txt.gz.tbi`

#3 versions_gatk4 tuple

`${task.process}` string	The name of the process
`gatk4` string	The name of the tool
`gatk --version \| sed -n '/GATK.v/s/.v//p'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
gatk4	Genome Analysis Toolkit (GATK4)	https://gatk.broadinstitute.org/hc/en-us

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:43:09 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fgatk4%2Fsitedepthtobaf/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/gatk4/sitedepthtobaf/blobs/sha256:9ad678c6524e2d18d7fc2a39b763de7e4ed36dbecf728281fed40f485b7215e5
Size	3.4 KB
Checksum	sha256:9ad678c6524e2d18d7fc2a39b763de7e4ed36dbecf728281fed40f485b7215e5
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:43:09 (UTC)		1	3.4 KB	-