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

nf-core/hiphase @ 0.0.0-6c4ed3a

Small and structural variant phasing tool for PacBio HiFi reads, supporting co-phasing of SNVs and SVs across multiple BAM files and samples

Latest version: 0.0.0-6c4ed3a

Total downloads: 2

Source: nf-core/modules

Authors: @tanyasarkjain @fellen31

Maintainers: @fellen31

Small and structural variant phasing tool for PacBio HiFi reads, supporting co-phasing of SNVs and SVs across multiple BAM files and samples

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

include { HIPHASE } from 'nf-core/hiphase'

MIT License

Process

`Name`	`HIPHASE`

Input 8 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`bams` file	One or more sorted BAM/CRAM files `*.{bam,cram}`
`bais` file	Index files associated with the BAM/CRAM files `*.{bai,crai,csi}`
`snv` file	Compressed VCF file containing SNV/small variants to phase (optional) `*.{vcf.gz}`
`snv_index` file	Index file for the SNV VCF (optional) `*.{tbi,csi}`
`sv` file	Compressed VCF file containing structural variants to co-phase (optional) `*.{vcf.gz}`
`sv_index` file	Index file for the SV VCF (optional) `*.{tbi,csi}`
`samples` list	List of sample names to phase within the VCF, if empty only the first sample is phased.

#2 tuple

`meta2` map	Groovy Map containing reference genome information e.g. `[ id:'GRCh38' ]`
`fasta` file	Reference genome FASTA file used for the BAM alignment `*.{fasta,fa}`
`fai` file	FASTA index file (.fai) for the reference genome `*.fai`

`output_bam` boolean	Whether to output haplotagged BAM files. Set to true to emit phased BAM files with haplotag information.

`summary_file` boolean	Whether to output a phasing summary file.

`blocks_file` boolean	Whether to output a phasing blocks file.

`stats_file` boolean	Whether to output a per-read phasing statistics file.

`haplotag_file` boolean	Whether to output a haplotag assignments file.

`file_format` string	Output file format for summary/blocks/stats/haplotag files, either 'tsv' or 'csv'.

Output 15 channels

#1 bams tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*.bam` file	Haplotagged BAM file(s) with haplotype information in the HP tag (optional, only emitted when output_bam is true) `*.bam`

#2 vcfs tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*_snv_phased.vcf.gz` file	Phased and compressed SNV VCF file (optional, only emitted when SNV VCF input is provided) `*_snv_phased.vcf.gz`

#3 sv_vcfs tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*_sv_phased.vcf.gz` file	Phased and compressed SV VCF file (optional, only emitted when SV VCF input is provided) `*_sv_phased.vcf.gz`

#4 stats_csv tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*.stats.csv` file	CSV file containing per-read phasing statistics (optional) `*.stats.csv`

#5 stats_tsv tuple

`meta` map