Nextflow Registry | nf-core/happy/sompy@0.0.0-6c4ed3a

nf-core/happy/sompy @ 0.0.0-6c4ed3a

Hap.py is a tool to compare diploid genotypes at haplotype level. som.py is a part of hap.py compares somatic variations.

happy sompy benchmark haplotype validation somatic variants

Latest version: 0.0.0-6c4ed3a

Total downloads: 9

Source: nf-core/modules

Authors: @kubranarci

Hap.py is a tool to compare diploid genotypes at haplotype level. som.py is a part of hap.py compares somatic variations.

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

include { HAPPY_SOMPY } from 'nf-core/happy/sompy'

MIT License

Process

`Name`	`HAPPY_SOMPY`

Input 6 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`query_vcf` file	VCF/GVCF file to query `*.{gvcf,vcf}.gz`
`truth_vcf` file	gold standard VCF file `*.{gvcf,vcf}.gz`
`regions_bed` file	Sparse regions to restrict the analysis to `*.bed`
`targets_bed` file	Dense regions to restrict the analysis to `*.bed`

#2 tuple

`meta2` map	Groovy Map containing fasta file information e.g. [ id:'test2']
`fasta` file	FASTA file of the reference genome `*.{fa,fasta}`

#3 tuple

`meta3` map	Groovy Map containing fai file information e.g. [ id:'test3']
`fasta_fai` file	The index of the reference FASTA `*.fai`

#4 tuple

`meta4` map	Groovy Map containing false_positives_bed file information e.g. [ id:'test4']
`false_positives_bed` file	False positive / confident call regions. Calls outside these regions will be labelled as UNK. `*.{bed,bed.gz}`

#5 tuple

`meta5` map	Groovy Map containing ambiguous_beds file information e.g. [ id:'test5']
`ambiguous_beds` file	Ambiguous regions `*.{bed,bed.gz}`

#6 tuple

`meta6` map	Groovy Map containing bam file information e.g. [ id:'test6']
`bams` file	one or more BAM files for feature table extraction `*.bam`

Output 4 channels

#1 stats tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.stats.csv` file	One or more than one (if AF count is on ) CSV file with benchmark stats `*.stats.csv`

#2 metrics tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.metrics.json` file	One or more than one (if AF count is on ) JSON file with metrics `*.metrics.json`

#3 features tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.features.csv` file	One or more than one (if AF count is on ) CSV file containing feature information `*.features.csv`

#4 versions_happy tuple

`${task.process}` string	The process the versions were collected from
`happy` string	The tool name
`0.3.15` string	The expression to obtain the version of the tool

Tool	Description	Homepage
sompy	Haplotype VCF comparison tools somatic variant comparison	https://www.illumina.com/products/by-type/informatics-products/basespace-sequence-hub/apps/hap-py-benchmarking.html

Version	0.0.0-6c4ed3a