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’]

inputs (file)

One or more input BAM/CRAM file(s)

*.{bam,cram}

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

vcf (file)

The called VCF file created by Gridss’ call step

*.vcf.gz