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}

meta2

:map

Groovy Map containing reference information

fasta

:file

The reference fasta

*.{fa,fna,fasta}

meta3

:map

Groovy Map containing reference information

fasta_fai

:file

The index of the reference fasta

*.fai

meta4

:map

Groovy Map containing reference information

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

vcf

meta

:map

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

*.vcf.gz

:file

The called VCF file created by Gridss’ call step

*.vcf.gz

versions_gridss

${task.process}

:string

The process

gridss

:string

The tool name

GeneratePonBedpe --version 2>&1 | sed 's/-gridss//'

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions

${task.process}

:string

The process

gridss

:string

The tool name

GeneratePonBedpe --version 2>&1 | sed 's/-gridss//'

:eval

The expression to obtain the version of the tool

Tools

maintainer
Github user nvnieuwk
get in touch
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