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

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

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: 0.0.0-0c7146d

Total downloads: 2

Source: nf-core/modules

Authors: @abhi18av @ramprasadn @fa2k

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_POSTPROCESSVARIANTS } from 'nf-core/deepvariant/postprocessvariants'

MIT License

Process

`Name`	`DEEPVARIANT_POSTPROCESSVARIANTS`

Input 4 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`variant_calls_tfrecord_files` file	One or more data files containing variant calls from DEEPVARIANT_CALLVARIANTS `*.tfrecord.gz`
`gvcf_tfrecords` file	Sharded tfrecord file from DEEPVARIANT_MAKEEXAMPLES with the coverage information used for GVCF output `*.gz`
`small_model_calls` file	Sharded tfrecord file from DEEPVARIANT_MAKEEXAMPLES with variant calls from the small model `*.gz`
`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 `*.gzi`

Output 5 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 vcf_index tuple

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

#4 gvcf_index tuple

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

#5 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