Nextflow Registry | nf-core/truvari/bench@0.0.0-6c4ed3a

nf-core/truvari/bench @ 0.0.0-6c4ed3a

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

structural variants sv vcf benchmark comparison

Latest version: 0.0.0-6c4ed3a

Total downloads: 9

Source: nf-core/modules

Authors: @nvnieuwk

Maintainers: @nvnieuwk

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

Add the following snippet to your workflow script to include this module.

include { TRUVARI_BENCH } from 'nf-core/truvari/bench'

MIT License

Process

`Name`	`TRUVARI_BENCH`

Input 3 channels

#1 tuple

`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`

#2 tuple

`meta2` map	Groovy Map containing fasta information e.g. `[ id:'test' ]`
`fasta` file	Reference FASTA file `*.{fasta,fa,fna}`

#3 tuple

`meta3` map	Groovy Map containing fasta index information e.g. `[ id:'test' ]`
`fai` file	Reference FASTA index file `*.fai`

Output 11 channels

#1 log tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test' ]`
`*.log.txt` file	Log file from Truvari run `*.log.txt`

#2 fn_tbi tuple

`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`

#3 fn_vcf tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test' ]`
`*.fn.vcf.gz` file	VCF file with false negatives `*.fn.vcf.gz`

#4 fp_tbi tuple

`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`

#5 fp_vcf tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test' ]`
`*.fp.vcf.gz` file	VCF file with false positives `*.fp.vcf.gz`

#6 summary tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test' ]`
`*.summary.json` file	Summary JSON file with results from the benchmark `*.summary.json`

#7 tp_base_tbi tuple

`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`

#8 tp_base_vcf tuple

`*.tp-base.vcf.gz` file
`meta` map	Groovy Map containing sample information e.g. `[ id:'test' ]`