Nextflow Registry | nf-core/sentieon/haplotyper@0.0.0-6c4ed3a

nf-core/sentieon/haplotyper @ 0.0.0-6c4ed3a

Runs Sentieon's haplotyper for germline variant calling.

sentieon haplotypecaller haplotype

Latest version: 0.0.0-6c4ed3a

Total downloads: 5

Source: nf-core/modules

Authors: @asp8200

Maintainers: @asp8200

Summary

Runs Sentieon's haplotyper for germline variant calling.

Get started

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

include { SENTIEON_HAPLOTYPER } from 'nf-core/sentieon/haplotyper'

License

MIT License

Process

`Name`	`SENTIEON_HAPLOTYPER`

Input 7 channels

#1 tuple

`meta` map	Groovy Map containing reference 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)
`recal_table` file	Recalibration table from sentieon/qualcal (optional)

#2 tuple

`meta2` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`fasta` file	Genome fasta file `*.{fa,fasta}`

#3 tuple

`meta3` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`fai` file	The index of the FASTA reference. `*.fai`

#4 tuple

`meta4` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`dbsnp` file	VCF file containing known sites (optional)

#5 tuple

`meta5` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`dbsnp_tbi` file	VCF index of dbsnp (optional)

`emit_vcf` string	Controls the vcf output from the haplotyper. If emit_vcf is set to "all" then the haplotyper will output a vcf generated by the haplotyper in emit-mode "all". If emit_vcf is set to "confident" then the haplotyper will output a vcf generated by the haplotyper in emit-mode "confident". If emit_vcf is set to "variant" then the haplotyper will output a vcf generated by the haplotyper in emit_mode "confident".

emit_vcf string

Controls the vcf output from the haplotyper. If emit_vcf is set to "all" then the haplotyper will output a vcf generated by the haplotyper in emit-mode "all". If emit_vcf is set to "confident" then the haplotyper will output a vcf generated by the haplotyper in emit-mode "confident". If emit_vcf is set to "variant" then the haplotyper will output a vcf generated by the haplotyper in emit_mode "confident".

`emit_gvcf` boolean	If true, the haplotyper will output a gvcf

Output 5 channels

#1 vcf tuple

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

#2 gvcf tuple

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

#3 vcf_tbi tuple

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

#4 gvcf_tbi tuple

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

#5 versions_sentieon tuple

`${task.process}` string	The process the versions were collected from
`sentieon` string	The tool name
`sentieon driver --version \| sed "s/.*-//g"` string	The command used to generate the version of the tool