Nextflow Registry | nf-core/dysgu/run@0.0.0-e2d3f0d

nf-core/dysgu/run @ 0.0.0-e2d3f0d

Dysgu calls structural variants (SVs) from mapped sequencing reads. It is designed for accurate and efficient detection of structural variations.

structural variants sv vcf

Latest version: 0.0.0-e2d3f0d

Total downloads: 2

Source: nf-core/modules

Authors: @famosab @poddarharsh15

Maintainers: @poddarharsh15 @nvnieuwk

Dysgu calls structural variants (SVs) from mapped sequencing reads. It is designed for accurate and efficient detection of structural variations.

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

include { DYSGU_RUN } from 'nf-core/dysgu/run'

MIT License

Process

`Name`	`DYSGU_RUN`

Input 7 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`input` file	Input BAM file `*.{bam,cram}`
`index` file	BAM index file `*.{bai,crai}`

#2 tuple

`meta2` map	Groovy Map containing reference information e.g. [ id:'genome' ]
`fasta` file	Genome reference FASTA file `*.{fa,fasta}`

#3 tuple

`meta3` map	Groovy Map containing reference information e.g. [ id:'genome' ]
`fai` file	Genome reference FASTA index file `*.{fa.fai,fasta.fai}`

#4 tuple

`meta4` map	Groovy Map containing reference information e.g. [ id:'genome' ]
`sites` file	Known sites VCF file `*.{vcf,vcf.gz}`

#5 tuple

`meta5` map	Groovy Map containing reference information e.g. [ id:'genome' ]
`bed` file	Regions to include BED file `*.bed`

#6 tuple

`meta6` map	Groovy Map containing reference information e.g. [ id:'genome' ]
`search_bed` file	Regions to search BED file `*.bed`

#7 tuple

`meta7` map	Groovy Map containing reference information e.g. [ id:'genome' ]
`exclude_bed` file	Regions to exclude BED file `*.bed`

Output 3 channels

#1 tbi tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'sample1' ]
`*.vcf.gz.tbi` file	The index of the BCF/VCF file `*.vcf.gz.tbi`

#2 vcf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'sample1' ]
`*.vcf.gz` file	VCF file with identified structural variants `*.{vcf.gz}`

#3 versions_dysgu tuple

`${task.process}` string	The name of the process
`dysgu` string	The name of the tool
`dysgu --version 2>&1 \| sed 's/.*version //'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
dysgu	Structural variant caller for mapped sequencing data	https://github.com/kcleal/dysgu