modules/svaba

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

svstructural variantsdetecting svsshort-read sequencing

https://github.com/nf-core/modules/[...]/modules/nf-core/svaba

Description

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

Input

name:type

description

pattern

`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}

`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}

`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}

`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}

`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

`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

`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

name:type

description

pattern