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

nf-core/multivcfanalyzer @ 0.0.0-6c4ed3a

SNP table generator from GATK UnifiedGenotyper with functionality geared for aDNA

vcf ancient DNA aDNA SNP GATK UnifiedGenotyper SNP table

Latest version: 0.0.0-6c4ed3a

Total downloads: 7

Source: nf-core/modules

Authors: @jfy133

Maintainers: @jfy133 @TCLamnidis

SNP table generator from GATK UnifiedGenotyper with functionality geared for aDNA

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

include { MULTIVCFANALYZER } from 'nf-core/multivcfanalyzer'

MIT License

Process

`Name`	`MULTIVCFANALYZER`

Input 10 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`vcfs` file	One or a list of gzipped or uncompressed VCF file `*.vcf`

#2 tuple

`meta2` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`fasta` file	Reference genome VCF was generated against `*.{fasta,fna,fa}`

#3 tuple

`meta3` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`snpeff_results` file	Results from snpEff in txt format (Optional) `*.txt`

#4 tuple

`meta4` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`gff` file	GFF file corresponding to reference genome fasta (Optional) `*.gff`

`allele_freqs` boolean	Whether to include the percentage of reads a given allele is present in in the SNP table.

`genotype_quality` integer	Minimum GATK genotyping threshold threshold of which a SNP call falling under is 'discarded'

`coverage` integer	Minimum number of a reads that a position must be covered by to be reported

`homozygous_freq` integer	Fraction of reads a base must have to be called 'homozygous'

`heterozygous_freq` integer	Fraction of which whereby if a call falls above this value, and lower than the homozygous threshold, a base will be called 'heterozygous'.

#10 tuple

`meta5` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`gff_exclude` file	file listing positions that will be 'filtered' (i.e. ignored) (Optional) `*.vcf`

Output 13 channels

#1 json tuple

`meta` map	Groovy Map containing sample information
`*MultiVCFAnalyzer.json` file	Summary statistics in MultiQC JSON format `.json`

#2 info_txt tuple

`meta` map	Groovy Map containing sample information
`*info.txt` file	Information about the run `.txt`

#3 snptable tuple

`meta` map	Groovy Map containing sample information
`*snpTable.tsv` file	Basic SNP table of combined positions taken from each VCF file `.tsv`

#4 snp_alignment tuple

`meta` map	Groovy Map containing sample information
`*snpAlignment.fasta.gz` file	A fasta file of just SNP positions with samples only `.fasta.gz`

#5 snpstatistics tuple

`meta` map	Groovy Map containing sample information
`*snpStatistics.tsv` file