modules/sentieon_dnascope

DNAscope algorithm performs an improved version of Haplotype variant calling.

dnascopesentieonvariant_calling

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

Description

DNAscope algorithm performs an improved version of Haplotype variant calling.

Input

name:type

description

pattern

`meta`
`:map`

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

`bam`
`:file`

BAM file.

*.bam

`bai`
`:file`

BAI file

*.bai

`intervals`
`:file`

bed or interval_list file containing interval in the reference that will be used in the analysis

*.{bed,interval_list}

`meta2`
`:map`

Groovy Map containing meta information for fasta.

`fasta`
`:file`

Genome fasta file

*.{fa,fasta}

`meta3`
`:map`

Groovy Map containing meta information for fasta index.

`fai`
`:file`

Index of the genome fasta file

*.fai

`meta4`
`:map`

Groovy Map containing meta information for dbsnp.

`dbsnp`
`:file`

Single Nucleotide Polymorphism database (dbSNP) file

*.vcf.gz

`meta5`
`:map`

Groovy Map containing meta information for dbsnp_tbi.

`dbsnp_tbi`
`:file`

Index of the Single Nucleotide Polymorphism database (dbSNP) file

*.vcf.gz.tbi

`meta6`
`:map`

Groovy Map containing meta information for machine learning model for Dnascope.

`ml_model`
`:file`

machine learning model file

*.model

`pcr_indel_model`
`:string`

Controls the option pcr_indel_model for Dnascope. The possible options are “NONE” (used for PCR free samples), and “HOSTILE”, “AGGRESSIVE” and “CONSERVATIVE”. See Sentieons documentation for further explanation.

`emit_vcf`
`:string`

Controls the vcf output from Dnascope. Possible options are “all”, “confident” and “variant”. See Sentieons documentation for further explanation.

`emit_gvcf`
`:boolean`

If true, the haplotyper will output a gvcf

Output

name:type

description

pattern

`vcf`

`meta`
`:map`

Groovy Map containing reference information. e.g. [ id:‘test’, single_end:false ]

`*.unfiltered.vcf.gz`
`:file`

Compressed VCF file

*.unfiltered.vcf.gz

`vcf_tbi`

`meta`
`:map`

Groovy Map containing reference information. e.g. [ id:‘test’, single_end:false ]

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

Index of VCF file

*.unfiltered.vcf.gz.tbi

`gvcf`

`meta`
`:map`

Groovy Map containing reference information. e.g. [ id:‘test’, single_end:false ]

`*.g.vcf.gz`
`:file`

Compressed GVCF file

*.g.vcf.gz

`gvcf_tbi`

`meta`
`:map`

Groovy Map containing reference information. e.g. [ id:‘test’, single_end:false ]

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

Index of GVCF file

*.g.vcf.gz.tbi

`versions_sentieon`

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

The process the versions were collected from

`sentieon`
`:string`

The tool name

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

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"`
`:string`

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_dnascope

Description

Input

meta:map

bam:file

bai:file

intervals:file

meta2:map

fasta:file

meta3:map

fai:file

meta4:map

dbsnp:file

meta5:map

dbsnp_tbi:file

meta6:map

ml_model:file

pcr_indel_model:string

emit_vcf:string

emit_gvcf:boolean

Output

vcf

meta:map

*.unfiltered.vcf.gz:file

vcf_tbi

meta:map

*.unfiltered.vcf.gz.tbi:file

gvcf

meta:map

*.g.vcf.gz:file

gvcf_tbi

meta:map

*.g.vcf.gz.tbi:file

versions_sentieon

${task.process}:string

sentieon:string

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

Topics

versions

${task.process}:string

sentieon:string

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

Tools

sentieon

included in

maintainer

get in touch

`meta`
`:map`

`bam`
`:file`

`bai`
`:file`

`intervals`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`:map`

`fai`
`:file`

`meta4`
`:map`

`dbsnp`
`:file`

`meta5`
`:map`

`dbsnp_tbi`
`:file`

`meta6`
`:map`

`ml_model`
`:file`

`pcr_indel_model`
`:string`

`emit_vcf`
`:string`

`emit_gvcf`
`:boolean`

`vcf`

`meta`
`:map`

`*.unfiltered.vcf.gz`
`:file`

`vcf_tbi`

`meta`
`:map`

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

`gvcf`

`meta`
`:map`

`*.g.vcf.gz`
`:file`

`gvcf_tbi`

`meta`
`:map`

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

`versions_sentieon`

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

`sentieon`
`:string`

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

`versions`

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

`sentieon`
`:string`

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