Nextflow Registry | nf-core/svanalyzer/svbenchmark@0.0.0-6c4ed3a

nf-core/svanalyzer/svbenchmark @ 0.0.0-6c4ed3a

SVbenchmark compares a set of “test” structural variants in VCF format to a known truth set (also in VCF format) and outputs estimates of sensitivity and specificity.

structural variant sv benchmarking

Latest version: 0.0.0-6c4ed3a

Total downloads: 9

Source: nf-core/modules

Authors: @kubranarci

Summary

SVbenchmark compares a set of “test” structural variants in VCF format to a known truth set (also in VCF format) and outputs estimates of sensitivity and specificity.

Get started

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

include { SVANALYZER_SVBENCHMARK } from 'nf-core/svanalyzer/svbenchmark'

License

MIT License

Process

`Name`	`SVANALYZER_SVBENCHMARK`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing test sample information e.g. `[ id:'test' ]`
`test` file	A VCF-formatted file of structural variants to test (required) `*.{vcf,vcf.gz}`
`test_tbi` file	A VCF-formatted file index of structural variants to test only for zipped files `*.{vcf.gz.tbi}`
`truth` file	A VCF-formatted file of variants to compare against (required) `*.{vcf,vcf.gz}`
`truth_tbi` file	A VCF-formatted file of variants to compare against only for zipped files `*.{vcf.gz.tbi}`
`bed` file	BED File of regions from which to include variants. Used to filter both test and truth variants. `*.{bed}`

#2 tuple

`meta2` map	Groovy Map containing reference genome information for fasta e.g. `[ id:'test2' ]`
`fasta` file	The reference FASTA file for the supplied VCF file or files (required) `*.{fa,fasta,fa.gz,fasta.gz}`

#3 tuple

`meta3` map	Groovy Map containing reference genome information for fai e.g. `[ id:'test3' ]`
`fai` file	The reference FASTA index file `*.{fai}`

Output 6 channels

#1 fns tuple

`meta` map	Groovy Map containing sample information inherited from test vcf e.g. `[ id:'test']`
`*.falsenegatives.vcf.gz` file	VCF file with False Negatives `*.{vcf.gz}`

#2 fps tuple

`meta` map	Groovy Map containing sample information inherited from test vcf e.g. `[ id:'test']`
`*.falsepositives.vcf.gz` file	VCF file with False Positives `*.{vcf.gz}`

#3 log tuple

`meta` map	Groovy Map containing sample information inherited from test vcf e.g. `[ id:'test']`
`*.log` file	LOG file of the run `*.{log}`

#4 report tuple

`meta` map	Groovy Map containing sample information inherited from test vcf e.g. `[ id:'test']`
`*.report` file	Text file reporting RECALL, PRECISION and F1. `*.{report}`

#5 distances tuple

`meta` map	Groovy Map containing sample information inherited from test vcf e.g. `[ id:'test']`
`*.distances` file	TSV file with genomic distances and size differences between structural variants compared `*.{distances}`

#6 versions_svanalyzer tuple

`${task.process}` string	The process the versions were collected from
`svanalyzer` string	The tool name
`0.36` string	The expression to obtain the version of the tool

Tool	Description	Homepage
svanalyzer	SVanalyzer: tools for the analysis of structural variation in genomes	https://svanalyzer.readthedocs.io/en/latest/index.html

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b