Nextflow Registry | nf-core/deepvariant/rundeepvariant@0.0.0-7f68141

nf-core/deepvariant/rundeepvariant @ 0.0.0-7f68141

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data

variant calling machine learning neural network

Latest version: 0.0.0-7f68141

Total downloads: 9

Source: nf-core/modules

Authors: @abhi18av @ramprasadn

Maintainers: @abhi18av @ramprasadn

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data

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

include { DEEPVARIANT_RUNDEEPVARIANT } from 'nf-core/deepvariant/rundeepvariant'

MIT License

Process

`Name`	`DEEPVARIANT_RUNDEEPVARIANT`

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	file containing intervals

#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 `*.gzi`

#5 tuple

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

Output 6 channels

#1 vcf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}.vcf.gz` file	Compressed VCF file `*.vcf.gz`

#2 gvcf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}.g.vcf.gz` file	Compressed GVCF file `*.g.vcf.gz`

#3 report tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}.visual_report.html` file	Visual report in HTML format `*.html`

#4 vcf_index tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}.vcf.gz.{tbi,csi}` file	Tabix index file of compressed VCF `*.vcf.gz.{tbi,csi}`

#5 gvcf_index tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}.g.vcf.gz.{tbi,csi}` file	Tabix index file of compressed GVCF `*.g.vcf.gz.{tbi,csi}`

#6 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