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

nf-core/paraphase @ 0.0.0-6c4ed3a

HiFi-based caller for highly homologous genes

paraphase long-read HiFi

Latest version: 0.0.0-6c4ed3a

Total downloads: 5

Source: nf-core/modules

Authors: @fellen31

Maintainers: @fellen31

HiFi-based caller for highly homologous genes

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

include { PARAPHASE } from 'nf-core/paraphase'

MIT License

Process

`Name`	`PARAPHASE`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:true ]`
`bam` file	Sorted BAM file `*.bam`
`bai` file	Index of BAM file `*.bai`

#2 tuple

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

#3 tuple

`meta3` map	Groovy Map containing config information e.g. [ id:'config' ]
`config` file	Config file `*.yaml`

Output 8 channels

#1 bai tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:true ]`
`*.paraphase.bam.bai` file	Index of (re)aligned BAM file `*.paraphase.bam.bai`

#2 bam tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:true ]`
`*.paraphase.bam` file	(re)aligned BAM file `*.paraphase.bam`

#3 vcf tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:true ]`
`${prefix}_paraphase_vcfs/*.vcf.gz` file	compressed VCF file(s) per gene `*.vcf.gz`

#4 json tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:true ]`
`*.paraphase.json` file	Summary of haplotype and variant calls `*.paraphase.json`

#5 vcf_index tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:true ]`
`${prefix}_paraphase_vcfs/*.vcf.gz.{csi,tbi}` file	compressed VCF file index `*.vcf.gz.{tbi,csi}`

#6 versions_minimap2 tuple

`${task.process}` string	The name of the process
`minimap2` string	The name of the tool
`minimap2 --version` eval	The expression to obtain the version of the tool

#7 versions_samtools tuple

`${task.process}` string	The name of the process
`samtools` string	The name of the tool
`samtools version \| sed '1!d;s/.* //'` eval	The expression to obtain the version of the tool

#8 versions_paraphase tuple

`${task.process}` string	The name of the process
`paraphase` string	The name of the tool
`paraphase --version` eval	The expression to obtain the version of the tool

Tool	Description	Homepage