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’]

vcf:file

GRIDSS generated vcf file

*.vcf

bedpe:file

GRIDSS generated bedpe file

*.bedpe

bed:file

GRIDSS generated bed file

*.bed

meta2:map

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

fasta:file

The reference fasta

*.{fa,fna,fasta}

meta3:map

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

fai:file

The index of the reference fasta

*.fai

meta4:map

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

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

bedpe

meta:map

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

*.bedpe:file

GRIDSS generated breakpoint pon bedpe file

*.bedpe

bed

meta:map

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

*.bed:file

GRIDSS generated breakpoint pon bed file

*.bed

versions

versions.yml:file

File containing software versions

versions.yml

Tools

maintainer
Github user kubranarci
get in touch
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