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

nf-core/freebayes @ 0.0.0-6c4ed3a

A haplotype-based variant detector

Latest version: 0.0.0-6c4ed3a

Total downloads: 9

Source: nf-core/modules

Authors: @maxibor @FriederikeHanssen @maxulysse

Maintainers: @maxibor @FriederikeHanssen @maxulysse

A haplotype-based variant detector

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

include { FREEBAYES } from 'nf-core/freebayes'

MIT License

Process

`Name`	`FREEBAYES`

Input 6 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`input_1` file	BAM/CRAM/SAM file `*.{bam,cram,sam}`
`input_1_index` file	BAM/CRAM/SAM index file `*.{bai,crai}`
`input_2` file	BAM/CRAM/SAM file `*.{bam,cram,sam}`
`input_2_index` file	BAM/CRAM/SAM index file `*.{bai,crai}`
`target_bed` file	Optional - Limit analysis to targets listed in this BED-format FILE. `*.bed`

#2 tuple

`meta2` map	Groovy Map containing reference information. e.g. [ id:'test_reference' ]
`fasta` file	reference fasta file `.{fa,fa.gz,fasta,fasta.gz}`

#3 tuple

`meta3` map	Groovy Map containing reference information. e.g. [ id:'test_reference' ]
`fasta_fai` file	reference fasta file index `*.{fa,fasta}.fai`

#4 tuple

`meta4` map	Groovy Map containing meta information for the samples file. e.g. [ id:'test_samples' ]
`samples` file	Optional - Limit analysis to samples listed (one per line) in the FILE. `*.txt`

#5 tuple

`meta5` map	Groovy Map containing meta information for the populations file. e.g. [ id:'test_populations' ]
`populations` file	Optional - Each line of FILE should list a sample and a population which it is part of. `*.txt`

#6 tuple

`meta6` map	Groovy Map containing meta information for the cnv file. e.g. [ id:'test_cnv' ]
`cnv` file	A copy number map BED file, which has either a sample-level ploidy: sample_name copy_number or a region-specific format: seq_name start end sample_name copy_number `*.bed`

Output 2 channels

#1 vcf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.vcf.gz` file	Compressed VCF file `*.vcf.gz`

#2 versions_freebayes tuple

`${task.process}` string	The name of the process
`freebayes` string	The name of the tool
`freebayes --version 2>&1 \| sed "s/version:\s*v//g"` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
freebayes	Bayesian haplotype-based polymorphism discovery and genotyping	https://github.com/freebayes/freebayes