Nextflow Registry | nf-core/rtgtools/bndeval@0.0.0-6c4ed3a

nf-core/rtgtools/bndeval @ 0.0.0-6c4ed3a

The bndeval tool of RTG tools. It is used to evaluate called BND type of variants for agreement with a BND baseline variant set

benchmarking vcf rtg-tools bnd-eval structural-variants

Latest version: 0.0.0-6c4ed3a

Total downloads: 7

Source: nf-core/modules

Authors: @kubranarci

Maintainers: @kubranarci

The bndeval tool of RTG tools. It is used to evaluate called BND type of variants for agreement with a BND baseline variant set

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

include { RTGTOOLS_BNDEVAL } from 'nf-core/rtgtools/bndeval'

MIT License

Process

`Name`	`RTGTOOLS_BNDEVAL`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`query_vcf` file	A VCF with called variants to benchmark against the standard `*.{vcf,vcf.gz}`
`query_vcf_tbi` file	The index of the VCF file with called variants to benchmark against the standard `*.{vcf.gz.tbi, vcf.tbi}`
`truth_vcf` file	A standard VCF to compare against `*.{vcf,vcf.gz}`
`truth_vcf_tbi` file	The index of the standard VCF to compare against `*.{vcf.gz.tbi, vcf.tbi}`
`regions_bed` file	A BED file containing the regions where bndeval will evaluate every fully and partially overlapping variant (optional) This input should be used to provide the regions used by the analysis `*.bed`

Output 11 channels

#1 fn_tbi tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.fn.vcf.gz.tbi` file	The index of the VCF file for the false negative variants `*.fn.vcf.gz.tbi`

#2 fn_vcf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.fn.vcf.gz` file	A VCF file for the false negative variants `*.fn.vcf.gz`

#3 fp_tbi tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.fp.vcf.gz.tbi` file	The index of the VCF file for the false positive variants `*.fp.vcf.gz.tbi`

#4 fp_vcf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.fp.vcf.gz` file	A VCF file for the false positive variants `*.fp.vcf.gz`

#5 tp_tbi tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.tp.vcf.gz.tbi` file	The index of the VCF file for the true positive variants `*.tp.vcf.gz.tbi`

#6 tp_vcf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.tp.vcf.gz` file	A VCF file for the true positive variants `*.tp.vcf.gz`

#7 summary tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.summary.txt` file	A TXT file containing the summary of the evaluation `*.summary.txt`

#8 baseline_tbi tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.tp-baseline.vcf.gz.tbi` file	The index of the VCF file for the true positive variants from the baseline `*.tp-baseline.vcf.gz.tbi`

#9 baseline_vcf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.tp-baseline.vcf.gz` file	A VCF file for the true positive variants from the baseline `*.tp-baseline.vcf.gz`

#10 weighted_roc tuple