modules/gatk4_svcluster

Clusters structural variants based on coordinates, event type, and supporting algorithms

gatk4structural variantssvclustervcf

https://github.com/nf-core/modules/[...]/modules/nf-core/gatk4/svcluster

Description

Clusters structural variants based on coordinates, event type, and supporting algorithms

Input

name:type

description

pattern

`meta`
`:map`

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

`vcfs`
`:file`

One or more VCF files created with a structural variant caller

*.vcf.gz

`indices`
`:file`

Index files for the VCFs

*.vcf.gz.tbi

`ploidy_table`
`:file`

The sample ploidy table

*.tsv

`fasta`
`:file`

Reference FASTA file needed when the input is a CRAM file

*.{fasta,fa}

`fasta_fai`
`:file`

Index of the reference FASTA file needed when the input is a CRAM file

*.fai

`dict`
`:file`

Sequence dictionary of the reference FASTA file needed when the input is a CRAM file

*.dict

Output

name:type

description

pattern

`clustered_vcf`

`meta`
`:map`

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

`*.vcf.gz`
`:file`

The VCF containing the clustered VCFs

*.vcf.gz

`clustered_vcf_index`

`meta`
`:map`

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

`*.vcf.gz.tbi`
`:file`

The index of the VCF containing the clustered VCFs

*.vcf.gz.tbi

`versions_gatk4`

`${task.process}`
`:string`

The name of the process

`gatk4`
`:string`

The name of the tool

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`gatk4`
`:string`

The name of the tool

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

The expression to obtain the version of the tool

Tools

gatk4
Apache-2.0

Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.

gatk.broadinstitute.org/hc/en-us github.com/broadinstitute/gatk 10.1158/1538-7445.AM2017-3590

modules/gatk4_svcluster

Description

Input

`meta`
`:map`

`vcfs`
`:file`

`indices`
`:file`

`ploidy_table`
`:file`

`fasta`
`:file`

`fasta_fai`
`:file`

`dict`
`:file`

Output

`clustered_vcf`

`meta`
`:map`

`*.vcf.gz`
`:file`

`clustered_vcf_index`

`meta`
`:map`

`*.vcf.gz.tbi`
`:file`

`versions_gatk4`

`${task.process}`
`:string`

`gatk4`
`:string`

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

Topics

`versions`

`${task.process}`
`:string`

`gatk4`
`:string`

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

Tools

gatk4
Apache-2.0

maintainer

get in touch

modules/gatk4_svcluster

Description

Input

meta:map

vcfs:file

indices:file

ploidy_table:file

fasta:file

fasta_fai:file

dict:file

Output

clustered_vcf

meta:map

*.vcf.gz:file

clustered_vcf_index

meta:map

*.vcf.gz.tbi:file

versions_gatk4

${task.process}:string

gatk4:string

gatk --version | sed -n '/GATK.*v/s/.*v//p':eval

Topics

versions

${task.process}:string

gatk4:string

gatk --version | sed -n '/GATK.*v/s/.*v//p':eval

Tools

gatk4 Apache-2.0

maintainer

get in touch

`meta`
`:map`

`vcfs`
`:file`

`indices`
`:file`

`ploidy_table`
`:file`

`fasta`
`:file`

`fasta_fai`
`:file`

`dict`
`:file`

`clustered_vcf`

`meta`
`:map`

`*.vcf.gz`
`:file`

`clustered_vcf_index`

`meta`
`:map`

`*.vcf.gz.tbi`
`:file`

`versions_gatk4`

`${task.process}`
`:string`

`gatk4`
`:string`

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

`versions`

`${task.process}`
`:string`

`gatk4`
`:string`

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

gatk4
Apache-2.0