Nextflow Registry | nf-core/bcftools/convert@0.0.0-6c4ed3a

nf-core/bcftools/convert @ 0.0.0-6c4ed3a

Converts certain output formats to VCF

bcftools convert vcf gvcf

Latest version: 0.0.0-6c4ed3a

Total downloads: 9

Source: nf-core/modules

Authors: @nvnieuwk @ramprasadn @atrigila

Maintainers: @nvnieuwk @ramprasadn @atrigila

Converts certain output formats to VCF

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

include { BCFTOOLS_CONVERT } from 'nf-core/bcftools/convert'

MIT License

Process

`Name`	`BCFTOOLS_CONVERT`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`input` file	The input format. Each format needs a separate parameter to be specified in the `args`: GEN/SAMPLE file: `--gensample2vcf` gVCF file: `--gvcf2vcf` HAP/SAMPLE file: `--hapsample2vcf` HAP/LEGEND/SAMPLE file: `--haplegendsample2vcf` TSV file: `--tsv2vcf` `*.{gen,sample,g.vcf,hap,legend}{.gz,}`
`input_index` file	(Optional) The index for the input files, if needed `*.bed`

#2 tuple

`meta2` map	Groovy Map containing reference information e.g. [ id:'genome' ]
`fasta` file	(Optional) The reference fasta, only needed for gVCF conversion `*.{fa,fasta}`

`bed` file	(Optional) The BED file containing the regions for the VCF file `*.bed`

Output 10 channels

#1 bcf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.bcf` file	BCF merged output file => when `--output-type u` is used `*.bcf`

#2 csi tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.csi` file	Default VCF file index `*.csi`

#3 hap tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.hap.gz` file	hap format used by IMPUTE2 and SHAPEIT `*.hap.gz`

#4 tbi tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.tbi` file	Alternative VCF file index `*.tbi`

#5 vcf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.vcf` file	VCF merged output file => when `--output-type v` is used `*.vcf`

#6 bcf_gz tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.bcf.gz` file	BCF merged output file (bgzipped) => when `--output-type b` is used `*.bcf.gz`

#7 legend tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.legend.gz` file	legend format used by IMPUTE2 and SHAPEIT `*.legend.gz`

#8 vcf_gz tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.vcf.gz` file	VCF merged output file (bgzipped) => when `--output-type z` is used `*.vcf.gz`

#9 samples tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.samples` file	samples format used by IMPUTE2 and SHAPEIT `*.samples`