Description

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

Input

name:type
description
pattern

meta{:bash}

:map

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

inputs{:bash}

:file

One or more input BAM/CRAM file(s)

*.{bam,cram}

meta2{:bash}

:map

Groovy Map containing reference information

fasta{:bash}

:file

The reference fasta

*.{fa,fna,fasta}

meta3{:bash}

:map

Groovy Map containing reference information

fasta_fai{:bash}

:file

The index of the reference fasta

*.fai

meta4{:bash}

:map

Groovy Map containing reference information

bwa_index{:bash}

:directory

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

Output

name:type
description
pattern

vcf{:bash}

meta{:bash}

:map

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

*.vcf.gz{:bash}

:file

The called VCF file created by Gridss’ call step

*.vcf.gz

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

maintainer
Github user nvnieuwk
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