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

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

TNscope algorithm performs somatic variant calling on the tumor-normal matched pair or the tumor only data, using a Haplotyper algorithm.

tnscope sentieon variant_calling

Latest version: 0.0.0-6c4ed3a

Total downloads: 6

Source: nf-core/modules

Authors: @ramprasadn

Maintainers: @ramprasadn

TNscope algorithm performs somatic variant calling on the tumor-normal matched pair or the tumor only data, using a Haplotyper algorithm.

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

include { SENTIEON_TNSCOPE } from 'nf-core/sentieon/tnscope'

MIT License

Process

`Name`	`SENTIEON_TNSCOPE`

Input 9 channels

#1 tuple

`meta` map	Groovy Map containing sample information. e.g. [ id:'test' ]
`input` file	One or more BAM or CRAM files. `*.{bam,cram}`
`input_index` file	Indices for the input files `*.{bai,crai}`
`intervals` file	bed or interval_list file containing interval in the reference that will be used in the analysis. Only recommended for large WGS data, else the overhead may not be worth the additional parallelisation. `*.{bed,interval_list}`

#2 tuple

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

#3 tuple

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

#4 tuple

`meta4` map	Groovy Map containing reference information. e.g. [ id:'test' ]
`dbsnp` file	Single Nucleotide Polymorphism database (dbSNP) file `*.vcf.gz`

#5 tuple

`meta5` map	Groovy Map containing reference information. e.g. [ id:'test' ]
`dbsnp_tbi` file	Index of the Single Nucleotide Polymorphism database (dbSNP) file `*.vcf.gz.tbi`

#6 tuple

`meta6` map	Groovy Map containing reference information. e.g. [ id:'test' ]
`pon` file	Single Nucleotide Polymorphism database (dbSNP) file `*.vcf.gz`

#7 tuple

`meta7` map	Groovy Map containing reference information. e.g. [ id:'test' ]
`pon_tbi` file	Index of the Single Nucleotide Polymorphism database (dbSNP) file `*.vcf.gz.tbi`

#8 tuple

`meta8` map	Groovy Map containing reference information. e.g. [ id:'test' ]
`cosmic` file	Catalogue of Somatic Mutations in Cancer (COSMIC) VCF file. `*.vcf.gz`

#9 tuple

`meta9` map	Groovy Map containing reference information. e.g. [ id:'test' ]
`cosmic_tbi` file	Index of the Catalogue of Somatic Mutations in Cancer (COSMIC) VCF file. `*.vcf.gz.tbi`

Output 3 channels

#1 vcf tuple

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

#2 index tuple

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

#3 versions_sentieon tuple

`sentieon`
`${task.process}` string	The process the versions were collected from