Description

GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements.

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’]

meta2 (map)

Groovy Map containing reference information
e.g. [ id:‘test’]

meta3 (map)

Groovy Map containing reference fai information
e.g. [ id:‘test’]

meta4 (map)

Groovy Map containing bwa generated index information
e.g. [ id:‘test’]

vcf (file)

GRIDSS generated vcf file

*.vcf

bedpe (file)

GRIDSS generated bedpe file

*.bedpe

bed (file)

GRIDSS generated bed file

*.bed

fasta (file)

The reference fasta

*.{fa,fna,fasta}

fasta_fai (file)

The index of the reference fasta

*.fai

bwa_index (directory)

OPTIONAL - The BWA index created from the reference fasta, will be generated by Gridss in the setupreference step

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’ ]

versions (file)

File containing software versions

versions.yml

bedpe (file)

GRIDSS generated breakpoint pon bedpe file

*.bedpe

bed (file)

GRIDSS generated breakpoint pon bed file

*.bed