Nextflow Registry | nf-core/deepvariant/makeexamples@0.0.0-0c7146d

nf-core/deepvariant/makeexamples @ 0.0.0-0c7146d

Transforms the input alignments to a format suitable for the deep neural network variant caller

variant calling machine learning neural network

Latest version: 0.0.0-0c7146d

Total downloads: 3

Source: nf-core/modules

Authors: @abhi18av @ramprasadn @fa2k

Maintainers: @abhi18av @ramprasadn

Transforms the input alignments to a format suitable for the deep neural network variant caller

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

include { DEEPVARIANT_MAKEEXAMPLES } from 'nf-core/deepvariant/makeexamples'

MIT License

Process

`Name`	`DEEPVARIANT_MAKEEXAMPLES`

Input 5 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`input` file	BAM/CRAM file `*.bam/cram`
`index` file	Index of BAM/CRAM file `*.bai/crai`
`intervals` file	Interval file for targeted regions `*.bed`

#2 tuple

`meta2` map	Groovy Map containing reference information e.g. [ id:'genome' ]
`fasta` file	The reference fasta file `*.fasta`

#3 tuple

`meta3` map	Groovy Map containing reference information e.g. [ id:'genome' ]
`fai` file	Index of reference fasta file `*.fai`

#4 tuple

`meta4` map	Groovy Map containing reference information e.g. [ id:'genome' ]
`gzi` file	GZI index of reference fasta file

#5 tuple

`meta5` map	Groovy Map containing reference information e.g. [ id:'genome' ] `*.gzi`
`par_bed` file	BED file containing PAR regions `*.bed`

Output 4 channels

#1 gvcf tuple

`meta` list	Tuple containing sample metadata and examples that can be used for calling
`${prefix}.gvcf.tfrecord--of-.gz` list	Tuple containing sample metadata and the GVCF data in tfrecord format

#2 examples tuple

`meta` list	Tuple containing sample metadata and examples that can be used for calling
`${prefix}.examples.tfrecord--of-.gz{,.example_info.json}` list	Tuple containing sample metadata and examples that can be used for calling

#3 small_model_calls tuple

`meta` list	Tuple containing sample metadata and examples that can be used for calling
`${prefix}_call_variant_outputs.examples.tfrecord--of-.gz` list	Optional variant calls from the small model, if enabled, in tfrecord format

#4 versions_deepvariant tuple

`${task.process}` string	The process the versions were collected from
`deepvariant` string	The tool name
`/opt/deepvariant/bin/run_deepvariant --version \| sed 's/^.*version //'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
deepvariant	DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data	https://github.com/google/deepvariant

Version	0.0.0-0c7146d
Commit ID	0c7146d85582628b5d1034504702fa808632b1af
Release Date	08 Apr 2026 18:57:16 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fdeepvariant%2Fmakeexamples/0.0.0-0c7146d/download