modules/truvari_bench

Given baseline and comparison sets of variants, calculate the recall/precision/f-measure

structural variantssvvcfbenchmarkcomparison

https://github.com/nf-core/modules/[...]/modules/nf-core/truvari/bench

Description

Given baseline and comparison sets of variants, calculate the recall/precision/f-measure

Input

name:type

description

pattern

`meta`
`:map`

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

`vcf`
`:file`

Input SV VCF file

*.vcf.gz

`tbi`
`:file`

Input SV VCF index file

*.vcf.gz.tbi

`truth_vcf`
`:file`

Input VCF file with truth SVs

*.vcf.gz

`truth_tbi`
`:file`

Input VCF index file with truth SVs

*.vcf.gz.tbi

`bed`
`:file`

BED file containing regions to compare

*.bed

`meta2`
`:map`

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

`fasta`
`:file`

Reference FASTA file

*.{fasta,fa,fna}

`meta3`
`:map`

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

`fai`
`:file`

Reference FASTA index file

*.fai

Output

name:type

description

pattern

`fn_vcf`

`meta`
`:map`

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

`*.fn.vcf.gz`
`:file`

VCF file with false negatives

*.fn.vcf.gz

`fn_tbi`

`meta`
`:map`

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

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

VCF index file with false negatives

*.fn.vcf.gz.tbi

`fp_vcf`

`meta`
`:map`

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

`*.fp.vcf.gz`
`:file`

VCF file with false positives

*.fp.vcf.gz

`fp_tbi`

`meta`
`:map`

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

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

VCF index file with false positives

*.fp.vcf.gz.tbi

`tp_base_vcf`

`meta`
`:map`

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

`*.tp-base.vcf.gz`
`:file`

VCF file with base true positives

*.tp-base.vcf.gz

`tp_base_tbi`

`meta`
`:map`

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

`*.tp-base.vcf.gz.tbi`
`:file`

VCF index file with base true positives

*.tp-base.vcf.gz.tbi

`tp_comp_vcf`

`meta`
`:map`

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

`*.tp-comp.vcf.gz`
`:file`

VCF file with compared true positives

*.tp-comp.vcf.gz

`tp_comp_tbi`

`meta`
`:map`

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

`*.tp-comp.vcf.gz.tbi`
`:file`

VCF index file with compared true positives

*.tp-comp.vcf.gz.tbi

`summary`

`meta`
`:map`

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

`*.summary.json`
`:file`

Summary JSON file with results from the benchmark

*.summary.json

`log`

`meta`
`:map`

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

`*.log.txt`
`:file`

Log file from Truvari run

*.log.txt

`versions_truvari`

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

The process the versions were collected from

`truvari`
`:string`

The name of the tool

`truvari version | sed 's/Truvari v//'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The process the versions were collected from

`truvari`
`:string`

The name of the tool

`truvari version | sed 's/Truvari v//'`
`:eval`

The expression to obtain the version of the tool

Tools

truvari
MIT

Structural variant comparison tool for VCFs

github.com/ACEnglish/truvari github.com/acenglish/truvari/wiki https://github.com/ACEnglish/truvari 10.1186/s13059-022-02840-6

modules/truvari_bench

Description

Input

meta:map

vcf:file

tbi:file

truth_vcf:file

truth_tbi:file

bed:file

meta2:map

fasta:file

meta3:map

fai:file

Output

fn_vcf

meta:map

*.fn.vcf.gz:file

fn_tbi

meta:map

*.fn.vcf.gz.tbi:file

fp_vcf

meta:map

*.fp.vcf.gz:file

fp_tbi

meta:map

*.fp.vcf.gz.tbi:file

tp_base_vcf

meta:map

*.tp-base.vcf.gz:file

tp_base_tbi

meta:map

*.tp-base.vcf.gz.tbi:file

tp_comp_vcf

meta:map

*.tp-comp.vcf.gz:file

tp_comp_tbi

meta:map

*.tp-comp.vcf.gz.tbi:file

summary

meta:map

*.summary.json:file

log

meta:map

*.log.txt:file

versions_truvari

${task.process}:string

truvari:string

truvari version | sed 's/Truvari v//':eval

Topics

versions

${task.process}:string

truvari:string

truvari version | sed 's/Truvari v//':eval

Tools

truvari MIT

included in

maintainer

get in touch

`meta`
`:map`

`vcf`
`:file`

`tbi`
`:file`

`truth_vcf`
`:file`

`truth_tbi`
`:file`

`bed`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`:map`

`fai`
`:file`

`fn_vcf`

`meta`
`:map`

`*.fn.vcf.gz`
`:file`

`fn_tbi`

`meta`
`:map`

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

`fp_vcf`

`meta`
`:map`

`*.fp.vcf.gz`
`:file`

`fp_tbi`

`meta`
`:map`

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

`tp_base_vcf`

`meta`
`:map`

`*.tp-base.vcf.gz`
`:file`

`tp_base_tbi`

`meta`
`:map`

`*.tp-base.vcf.gz.tbi`
`:file`

`tp_comp_vcf`

`meta`
`:map`

`*.tp-comp.vcf.gz`
`:file`

`tp_comp_tbi`

`meta`
`:map`

`*.tp-comp.vcf.gz.tbi`
`:file`

`summary`

`meta`
`:map`

`*.summary.json`
`:file`

`log`

`meta`
`:map`

`*.log.txt`
`:file`

`versions_truvari`

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

`truvari`
`:string`

`truvari version | sed 's/Truvari v//'`
`:eval`

`versions`

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

`truvari`
`:string`

`truvari version | sed 's/Truvari v//'`
`:eval`

truvari
MIT