Nextflow Registry | nf-core/clair3@0.0.0-6c4ed3a

nf-core/clair3 @ 0.0.0-6c4ed3a

Clair3 is a germline small variant caller for long-reads

germline variant Indel SNV

Latest version: 0.0.0-6c4ed3a

Total downloads: 3

Source: nf-core/modules

Authors: @robert-a-forsyth

Maintainers: @robert-a-forsyth

Clair3 is a germline small variant caller for long-reads

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

include { CLAIR3 } from 'nf-core/clair3'

MIT License

Process

`Name`	`CLAIR3`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`bam` file	Sorted BAM/CRAM/SAM file `*.{bam,cram,sam}`
`bai` file	BAM index file `*.bai`
`packaged_model` string	string containing the name of a prepackaged Clair3 model full list of models and their descriptions is provided at https://github.com/HKU-BAL/Clair3?tab=readme-ov-file#pre-trained-models
`user_model` directory	directory containing Clair3 model files
`platform` string	val in ['hifi','ont', 'ilmn'] to indicate pacbio, ONT, or illumina respectively

#2 tuple

`meta2` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`reference` file	reference fasta file `*.fasta`

#3 tuple

`meta3` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`index` file	reference index file `*.fai`

Output 7 channels

#1 tbi tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]` `*.{vcf,vcf.gz}`
`${prefix}merge_output.vcf.gz.tbi` file	index for vcf files `*.{vcf.tbi,vcf.tbi.gz}`

#2 vcf tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]` `*.{vcf,vcf.gz}`
`${prefix}merge_output.vcf.gz` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]` `*.{vcf,vcf.gz}`

#3 gtbi tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]` `*.{vcf,vcf.gz}`
`${prefix}merge_output.gvcf.gz.tbi` file	index for gvcf file `*.{vcf.tbi,vcf.tbi.gz}`

#4 gvcf tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]` `*.{vcf,vcf.gz}`
`${prefix}merge_output.gvcf.gz` file	gvcf file `*.{gvcf,gvcf.gz}`

#5 phased_tbi tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]` `*.{vcf,vcf.gz}`
`${prefix}phased_merge_output.vcf.gz.tbi` file	index for vcf files `*.{vcf.tbi,vcf.tbi.gz}`

#6 phased_vcf tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]` `*.{vcf,vcf.gz}`
`${prefix}phased_merge_output.vcf.gz` file	phased vcf `*.{vcf,vcf.gz}`

#7 versions_clair3 tuple

`${task.process}` string	The name of the process
`clair3` string	The name of the tool
`run_clair3.sh --version \| sed "s/^Clair3 v//"` eval	The expression to obtain the version of the tool