Nextflow Registry | nf-core/sentieon/tnhaplotyper2@0.0.0-6c4ed3a

nf-core/sentieon/tnhaplotyper2 @ 0.0.0-6c4ed3a

Tnhaplotyper2 performs somatic variant calling on the tumor-normal matched pairs.

tnseq tnhaplotyper2 sentieon variant_calling

Latest version: 0.0.0-6c4ed3a

Total downloads: 8

Source: nf-core/modules

Authors: @asp8200

Maintainers: @asp8200

Tnhaplotyper2 performs somatic variant calling on the tumor-normal matched pairs.

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

include { SENTIEON_TNHAPLOTYPER2 } from 'nf-core/sentieon/tnhaplotyper2'

MIT License

Process

`Name`	`SENTIEON_TNHAPLOTYPER2`

Input 10 channels

#1 tuple

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

#2 tuple

`meta2` map	Groovy Map containing reference information. e.g. [ id:'test' ]
`dict` file	GATK sequence dictionary `*.dict`

#3 tuple

`meta3` map	Groovy Map containing reference information. e.g. [ id:'test' ]
`fasta` file	Genome fasta file `*.{fa,fasta}`

#4 tuple

`meta4` map	Groovy Map containing reference information. e.g. [ id:'test' ]
`fai` file	Index of the genome fasta file `*.fai`

#5 tuple

`meta5` map	Groovy Map containing reference information. e.g. [ id:'test' ]
`germline_resource` file	Population vcf of germline sequencing, containing allele fractions. `*.vcf.gz`

#6 tuple

`meta6` map	Groovy Map containing reference information. e.g. [ id:'test' ]
`germline_resource_tbi` file	Index file for the germline resource. `*.vcf.gz.tbi`

#7 tuple

`meta7` map	Groovy Map containing reference information. e.g. [ id:'test' ]
`panel_of_normals` file	vcf file to be used as a panel of normals. `*.vcf.gz`

#8 tuple

`meta8` map	Groovy Map containing reference information. e.g. [ id:'test' ]
`panel_of_normals_tbi` file	Index for the panel of normals. `*.vcf.gz.tbi`

`emit_orientation_data` boolean	If true, the module will run the sentieon algorithm TNhaplotyper2 followed by the sentieon algorithm OrientationBias.

`emit_contamination_data` boolean	If true, the module will run the sentieon algorithm TNhaplotyper2 followed by the sentieon algorithm ContaminationModel.

Output 7 channels

#1 vcf tuple

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

#2 index tuple

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

#3 stats tuple

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