Nextflow Registry | nf-core/severus@0.0.0-6c4ed3a

nf-core/severus @ 0.0.0-6c4ed3a

Severus is a somatic structural variation (SV) caller for long reads (both PacBio and ONT)

structural variation somatic germline long-read

Latest version: 0.0.0-6c4ed3a

Total downloads: 6

Source: nf-core/modules

Authors: @fellen31

Maintainers: @fellen31

Severus is a somatic structural variation (SV) caller for long reads (both PacBio and ONT)

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

include { SEVERUS } from 'nf-core/severus'

MIT License

Process

`Name`	`SEVERUS`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`target_input` file	path to one or multiple target BAM/CRAM files (e.g. tumor, must be indexed) `*.{bam,cram}`
`target_index` file	path to one or multiple target BAM/CRAM index files `*.{bai,crai,csi}`
`control_input` file	path to the control BAM/CRAM file (e.g. normal, must be indexed) `*.{bam,cram}`
`control_index` file	path to the control BAM/CRAM file index `*.{bai,crai,csi}`
`vcf` file	path to vcf file used for phasing (if using haplotype specific SV calling `*.{vcf,vcf.gz}`

#2 tuple

`meta2` map	Groovy Map containing tandem repeat regions information e.g. `[ id:'hg38']`
`bed` file	path to bed file for tandem repeat regions (must be ordered) `*.bed`

Output 16 channels

#1 log tuple

`meta` map	Groovy Map containing sample information
`${prefix}/severus.log` file	log file `${prefix}/severus.log`

#2 loh tuple

`meta` map	Groovy Map containing sample information
`${prefix}/severus_LOH.bed` file	BED file containing loss of heterozygosity information `${prefix}/severus_LOH.bed`

#3 all_vcf tuple

`meta` map	Groovy Map containing sample information
`${prefix}/all_SVs/severus_all.vcf` map	VCF file containing somatic and germline structural variants `${prefix}/all_SVs/severus_all.vcf`

#4 read_ids tuple

`meta` map	Groovy Map containing sample information
`${prefix}/read_ids.csv` file	Contains supporting read IDs for each SV `${prefix}/read_ids.csv`

#5 all_plots tuple

`meta` map	Groovy Map containing sample information
`${prefix}/all_SVs/plots/severus*.html` file	HTML files containing plots for all SVs `${prefix}/all_SVs/plots/severus*.html`

#6 read_qual tuple

`meta` map	Groovy Map containing sample information
`${prefix}/read_qual.txt` file	txt file containing read quality information `${prefix}/read_qual.txt`

#7 somatic_vcf tuple

`meta` map	Groovy Map containing sample information
`${prefix}/somatic_SVs/severus_somatic.vcf` file	VCF file containing somatic structural variants (SV) `${prefix}/somatic_SVs/severus_all.vcf`

#8 collapsed_dup tuple

`meta` map	Groovy Map containing sample information
`${prefix}/severus_collaped_dup.bed` file	BED file containing collapsed duplications `${prefix}/severus_collaped_dup`

#9 somatic_plots tuple

`meta` map