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

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

DNAscope algorithm performs an improved version of Haplotype variant calling.

dnascope sentieon variant_calling

Latest version: 0.0.0-6c4ed3a

Total downloads: 6

Source: nf-core/modules

Authors: @ramprasadn

Maintainers: @ramprasadn

DNAscope algorithm performs an improved version of Haplotype variant calling.

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

include { SENTIEON_DNASCOPE } from 'nf-core/sentieon/dnascope'

MIT License

Process

`Name`	`SENTIEON_DNASCOPE`

Input 9 channels

#1 tuple

`meta` map	Groovy Map containing sample information. e.g. [ id:'test', single_end:false ]
`bam` file	BAM file. `*.bam`
`bai` file	BAI file `*.bai`
`intervals` file	bed or interval_list file containing interval in the reference that will be used in the analysis `*.{bed,interval_list}`

#2 tuple

`meta2` map	Groovy Map containing meta information for fasta.
`fasta` file	Genome fasta file `*.{fa,fasta}`

#3 tuple

`meta3` map	Groovy Map containing meta information for fasta index.
`fai` file	Index of the genome fasta file `*.fai`

#4 tuple

`meta4` map	Groovy Map containing meta information for dbsnp.
`dbsnp` file	Single Nucleotide Polymorphism database (dbSNP) file `*.vcf.gz`

#5 tuple

`meta5` map	Groovy Map containing meta information for dbsnp_tbi.
`dbsnp_tbi` file	Index of the Single Nucleotide Polymorphism database (dbSNP) file `*.vcf.gz.tbi`

#6 tuple

`meta6` map	Groovy Map containing meta information for machine learning model for Dnascope.
`ml_model` file	machine learning model file `*.model`

`pcr_indel_model` string	Controls the option pcr_indel_model for Dnascope. The possible options are "NONE" (used for PCR free samples), and "HOSTILE", "AGGRESSIVE" and "CONSERVATIVE". See Sentieons documentation for further explanation.

`emit_vcf` string	Controls the vcf output from Dnascope. Possible options are "all", "confident" and "variant". See Sentieons documentation for further explanation.

`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