Nextflow Registry | nf-core/gatk4/haplotypecaller@0.0.0-6c4ed3a

nf-core/gatk4/haplotypecaller @ 0.0.0-6c4ed3a

Call germline SNPs and indels via local re-assembly of haplotypes

gatk4 haplotype haplotypecaller

Latest version: 0.0.0-6c4ed3a

Total downloads: 7

Source: nf-core/modules

Authors: @suzannejin @FriederikeHanssen

Maintainers: @suzannejin @FriederikeHanssen

Call germline SNPs and indels via local re-assembly of haplotypes

Add the following snippet to your workflow script to include this module.

include { GATK4_HAPLOTYPECALLER } from 'nf-core/gatk4/haplotypecaller'

MIT License

Process

`Name`	`GATK4_HAPLOTYPECALLER`

Input 6 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`input` file	BAM/CRAM file from alignment `*.{bam,cram}`
`input_index` file	BAI/CRAI file from alignment `*.{bai,crai}`
`intervals` file	Bed file with the genomic regions included in the library (optional)
`dragstr_model` file	Text file containing the DragSTR model of the used BAM/CRAM file (optional) `*.txt`

#2 tuple

`meta2` map	Groovy Map containing reference information e.g. [ id:'test_reference' ]
`fasta` file	The reference fasta file `*.fasta`

#3 tuple

`meta3` map	Groovy Map containing reference information e.g. [ id:'test_reference' ]
`fai` file	Index of reference fasta file `fasta.fai`

#4 tuple

`meta4` map	Groovy Map containing reference information e.g. [ id:'test_reference' ]
`dict` file	GATK sequence dictionary `*.dict`

#5 tuple

`meta5` map	Groovy Map containing dbsnp information e.g. [ id:'test_dbsnp' ]
`dbsnp` file	VCF file containing known sites (optional)

#6 tuple

`meta6` map	Groovy Map containing dbsnp information e.g. [ id:'test_dbsnp' ]
`dbsnp_tbi` file	VCF index of dbsnp (optional)

Output 4 channels

#1 bam tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.realigned.bam` file	Assembled haplotypes and locally realigned reads `*.realigned.bam`

#2 tbi tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.tbi` file	Index of VCF file `*.vcf.gz.tbi`

#3 vcf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.vcf.gz` file	Compressed VCF file `*.vcf.gz`

#4 versions_gatk4 tuple

`${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

Tool	Description	Homepage
gatk4	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.	https://gatk.broadinstitute.org/hc/en-us

Version	0.0.0-6c4ed3a