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

nf-core/svaba @ 0.0.0-6c4ed3a

SvABA is an efficient and accurate method for detecting SVs from short-read sequencing data using genome-wide local assembly with low memory and computing requirements

sv structural variants detecting svs short-read sequencing

Latest version: 0.0.0-6c4ed3a

Total downloads: 10

Source: nf-core/modules

Authors: @kubranarci

Maintainers: @kubranarci

Summary

SvABA is an efficient and accurate method for detecting SVs from short-read sequencing data using genome-wide local assembly with low memory and computing requirements

Get started

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

include { SVABA } from 'nf-core/svaba'

License

MIT License

Process

`Name`	`SVABA`

Input 7 channels

#1 tuple

`meta` map	Groovy Map containing sample information id: should be the identification number or sample name. If there is normal file meta should be common e.g. [ id:'test' ]
`tumorbam` file	Tumor or metastatic sample, BAM, SAM or CRAM file `*.{bam,cram,sam}`
`tumorbai` file	Index of the tumor or metastatic sample `*.{bai,crai,sai}`
`normalbam` file	Control (or normal) of matching tumor/metastatic sample, BAM, SAM or CRAM file `*.{bam,cram,sam}`
`normalbai` file	Index `*.{bai,crai,sai}`

#2 tuple

`meta2` map	Groovy Map containing FASTA information id: should be the identification number for alignment file and should be the same used to create BWA index files e.g. [ id:'fasta' ]
`fasta` file	FASTA file `*.{fasta\|fa}`

#3 tuple

`meta3` map	Groovy Map containing FASTA information id: should be the identification number for alignment file and should be the same used to create BWA index files e.g. [ id:'fasta' ]
`fasta_fai` file	Index of FASTA file `*.{fai}`

#4 tuple

`meta4` map	Groovy Map containing BWA information id: should be the identification number same as fasta file e.g. [ id:'bwa' ]
`bwa_index` file	BWA genome index files. Note that this tool requires the bwa index files to be of the format `prefix.suffix.amb`, where `prefix.suffix` is the full name of the fasta file, not just the prefix. `Directory containing BWA index *.{amb,ann,bwt,pac,sa}`

#5 tuple

`meta5` map	Groovy Map containing dbSNP information id: should be the identification number for dbSNP files e.g. [ id:'test' ]
`dbsnp` file	VCF file including dbSNP variants `*.vcf.gz`

#6 tuple

`meta6` map	Groovy Map containing dbSNP information id: should be the identification number for dbSNP files e.g. [ id:'test' ]
`dbsnp_tbi` file	Index of VCF file including dbSNP variants `*.vcf.gz.tbi`

#7 tuple

`meta7` map	Groovy Map containing regions information id: should be the identification number for regions e.g. [ id:'test' ]
`regions` file	Targeted intervals. Accepts BED file or Samtools-style string `.bed\|.txt\|*.tab`

Output 16 channels

#1 sv tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*.svaba.sv.vcf.gz` file	Filtered SVs for tumor only cases `*.vcf.gz`

#2 log tuple

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

#3 indel tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*.svaba.indel.vcf.gz` file	Filtered Indels for tumor only cases `*.vcf.gz`

#4 som_sv tuple

`*.svaba.somatic.sv.vcf.gz` file
`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]