modules/sentieon_dnamodelapply

modifies the input VCF file by adding the MLrejected FILTER to variants that are rejected by the selected machine learning model

dnamodelapplyvcffiltersentieon

https://github.com/nf-core/modules/[...]/modules/nf-core/sentieon/dnamodelapply

Description

modifies the input VCF file by adding the MLrejected FILTER to variants that are rejected by the selected machine learning model

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]

`vcf`
`:file`

INPUT VCF file

*.{vcf,vcf.gz}

`idx`
`:file`

Index of the input VCF file

*.{tbi}

`meta2`
`:map`

Groovy Map containing reference information e.g. [ id:'test' ]

`fasta`
`:file`

Genome fasta file

*.{fa,fasta}

`meta3`
`:map`

Groovy Map containing reference information e.g. [ id:'test' ]

`fai`
`:file`

Index of the genome fasta file

*.fai

`meta4`
`:map`

Groovy Map containing reference information e.g. [ id:'test' ]

`ml_model`
`:file`

machine learning model file

*.model

Output

name:type

description

pattern

`vcf`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]

`*.vcf.gz`
`:file`

Output VCF file

*.{vcf,vcf.gz}

`tbi`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]

`*.vcf.gz.tbi`
`:file`

Index of the output VCF file

*.{tbi}

`versions_sentieon`

`${task.process}`
`:string`

The process the versions were collected from

`sentieon`
`:string`

The tool name

`sentieon driver --version | sed "s/.*-//g"`
`:eval`

The command used to generate the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The process the versions were collected from

`sentieon`
`:string`

The tool name

`sentieon driver --version | sed "s/.*-//g"`
`:eval`

The command used to generate the version of the tool

Tools

sentieon

Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.

sentieon.com

modules/sentieon_dnamodelapply

Description

Input

`meta`
`:map`

`vcf`
`:file`

`idx`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`:map`

`fai`
`:file`

`meta4`
`:map`

`ml_model`
`:file`

Output

`vcf`

`meta`
`:map`

`*.vcf.gz`
`:file`

`tbi`

`meta`
`:map`

`*.vcf.gz.tbi`
`:file`

`versions_sentieon`

`${task.process}`
`:string`

`sentieon`
`:string`

`sentieon driver --version | sed "s/.*-//g"`
`:eval`

Topics

`versions`

`${task.process}`
`:string`

`sentieon`
`:string`

`sentieon driver --version | sed "s/.*-//g"`
`:eval`

Tools

sentieon

included in

maintainer

get in touch

modules/sentieon_dnamodelapply

Description

Input

meta :map

vcf :file

idx :file

meta2 :map

fasta :file

meta3 :map

fai :file

meta4 :map

ml_model :file

Output

vcf

meta :map

*.vcf.gz :file

tbi

meta :map

*.vcf.gz.tbi :file

versions_sentieon

${task.process} :string

sentieon :string

sentieon driver --version | sed "s/.*-//g" :eval

Topics

versions

${task.process} :string

sentieon :string

sentieon driver --version | sed "s/.*-//g" :eval

Tools

sentieon

included in

maintainer

get in touch

`meta`
`:map`

`vcf`
`:file`

`idx`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`:map`

`fai`
`:file`

`meta4`
`:map`

`ml_model`
`:file`

`vcf`

`meta`
`:map`

`*.vcf.gz`
`:file`

`tbi`

`meta`
`:map`

`*.vcf.gz.tbi`
`:file`

`versions_sentieon`

`${task.process}`
`:string`

`sentieon`
`:string`

`sentieon driver --version | sed "s/.*-//g"`
`:eval`

`versions`

`${task.process}`
`:string`

`sentieon`
`:string`

`sentieon driver --version | sed "s/.*-//g"`
`:eval`