Nextflow Registry | nf-core/sentieon/tnfilter@0.0.0-0c7146d

nf-core/sentieon/tnfilter @ 0.0.0-0c7146d

Filters the raw output of sentieon/tnhaplotyper2.

tnfilter filter sentieon tnhaplotyper2 vcf

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @asp8200

Filters the raw output of sentieon/tnhaplotyper2.

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

include { SENTIEON_TNFILTER } from 'nf-core/sentieon/tnfilter'

MIT License

Process

`Name`	`SENTIEON_TNFILTER`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`vcf` file	compressed vcf file from tnhaplotyper2 `*.vcf.gz`
`vcf_tbi` file	Tabix index of vcf file `*vcf.gz.tbi`
`stats` file	Stats file that pairs with output vcf file `*vcf.gz.stats`
`contamination` file	the location and file name of the file containing the contamination information produced by ContaminationModel. `*.contamination_data.tsv`
`segments` file	the location and file name of the file containing the tumor segments information produced by ContaminationModel. `*.segments`
`orientation_priors` file	the location and file name of the file containing the orientation bias information produced by OrientationBias. `*.orientation_data.tsv`

#2 tuple

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

#3 tuple

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

Output 4 channels

#1 tbi tuple

`meta` file	file containing filtered tnhaplotyper2 calls. `*.vcf.gz`
`*.vcf.gz.tbi` file	tbi file that pairs with vcf. `*.vcf.gz.tbi`

#2 vcf tuple

`meta` file	file containing filtered tnhaplotyper2 calls. `*.vcf.gz`
`*.vcf.gz` file	file containing filtered tnhaplotyper2 calls. `*.vcf.gz`

#3 stats tuple

`meta` file	file containing filtered tnhaplotyper2 calls. `*.vcf.gz`
`*.vcf.gz.stats` file	file containing statistics of the tnfilter run. `*.stats`

#4 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

Tool	Description	Homepage
sentieon	Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.	https://www.sentieon.com/

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:12:17 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fsentieon%2Ftnfilter/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/sentieon/tnfilter/blobs/sha256:8338ad77902d98e5a4e1e6105216f1fc4e514fc69212f77420eb5f16c28d3419
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