modules/sentieon_tnscope

TNscope algorithm performs somatic variant calling on the tumor-normal matched pair or the tumor only data, using a Haplotyper algorithm.

tnscopesentieonvariant_calling

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

Description

TNscope algorithm performs somatic variant calling on the tumor-normal matched pair or the tumor only data, using a Haplotyper algorithm.

Input

name:type

description

pattern

`meta`
`:map`

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

`input`
`:file`

One or more BAM or CRAM files.

*.{bam,cram}

`input_index`
`:file`

Indices for the input files

*.{bai,crai}

`intervals`
`:file`

bed or interval_list file containing interval in the reference that will be used in the analysis. Only recommended for large WGS data, else the overhead may not be worth the additional parallelisation.

*.{bed,interval_list}

`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’ ]

`dbsnp`
`:file`

Single Nucleotide Polymorphism database (dbSNP) file

*.vcf.gz

`meta5`
`:map`

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

`dbsnp_tbi`
`:file`

Index of the Single Nucleotide Polymorphism database (dbSNP) file

*.vcf.gz.tbi

`meta6`
`:map`

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

`pon`
`:file`

Single Nucleotide Polymorphism database (dbSNP) file

*.vcf.gz

`meta7`
`:map`

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

`pon_tbi`
`:file`

Index of the Single Nucleotide Polymorphism database (dbSNP) file

*.vcf.gz.tbi

`meta8`
`:map`

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

`cosmic`
`:file`

Catalogue of Somatic Mutations in Cancer (COSMIC) VCF file.

*.vcf.gz

`meta9`
`:map`

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

`cosmic_tbi`
`:file`

Index of the Catalogue of Somatic Mutations in Cancer (COSMIC) VCF file.

*.vcf.gz.tbi

Output

name:type

description

pattern

`vcf`

`meta`
`:map`

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

`*.vcf.gz`
`:file`

VCF file

*.{vcf.gz}

`index`

`meta`
`:map`

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

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

Index of the VCF file

*.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_tnscope

Description

Input

meta:map

input:file

input_index:file

intervals:file

meta2:map

fasta:file

meta3:map

fai:file

meta4:map

dbsnp:file

meta5:map

dbsnp_tbi:file

meta6:map

pon:file

meta7:map

pon_tbi:file

meta8:map

cosmic:file

meta9:map

cosmic_tbi:file

Output

vcf

meta:map

*.vcf.gz:file

index

meta:map

*.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`

`input`
`:file`

`input_index`
`:file`

`intervals`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`:map`

`fai`
`:file`

`meta4`
`:map`

`dbsnp`
`:file`

`meta5`
`:map`

`dbsnp_tbi`
`:file`

`meta6`
`:map`

`pon`
`:file`

`meta7`
`:map`

`pon_tbi`
`:file`

`meta8`
`:map`

`cosmic`
`:file`

`meta9`
`:map`

`cosmic_tbi`
`:file`

`vcf`

`meta`
`:map`

`*.vcf.gz`
`:file`

`index`

`meta`
`:map`

`*.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`