Nextflow Registry | nf-core/topas/gencons@0.0.0-6c4ed3a

nf-core/topas/gencons @ 0.0.0-6c4ed3a

Create fasta consensus with TOPAS toolkit with options to penalize substitutions for typical DNA damage present in ancient DNA

consensus fasta ancient DNA

Latest version: 0.0.0-6c4ed3a

Total downloads: 8

Source: nf-core/modules

Authors: @aidaanva

Maintainers: @aidaanva

Create fasta consensus with TOPAS toolkit with options to penalize substitutions for typical DNA damage present in ancient DNA

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

include { TOPAS_GENCONS } from 'nf-core/topas/gencons'

MIT License

Process

`Name`	`TOPAS_GENCONS`

Input 5 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`vcf` file	Gzipped compressed vcf file generated with GATK UnifiedGenotyper containing the called snps `*.vcf.gz`

#2 tuple

`meta2` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`vcf_indels` file	Optional gzipped compressed vcf file generated with GATK UnifiedGenotyper containing the called indels `*.vcf.gz`

#3 tuple

`meta3` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`reference` file	Fasta file of reference genome `*.fasta`

#4 tuple

`meta4` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`fai` file	Optional index for the fasta file of reference genome `*.fai`

`vcf_output` boolean	Boolean value to indicate if a compressed vcf file with the consensus calls included as SNPs should be produced

Output 5 channels

#1 ccf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.ccf` file	Statistics file containing information about the consensus calls in the fasta file `*.ccf`

#2 log tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.log` file	Log file `*.log`

#3 vcf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.vcf.gz` file	Gzipped vcf file with updated calls for the SNPs used in the consensus generation and for bases under threshold replaced with Ns `*.vcf.gz`

#4 fasta tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.fasta.gz` file	Gzipped consensus fasta file with bases under threshold replaced with Ns `*.fasta.gz`

#5 versions

`versions.yml` file	File containing software versions `versions.yml`

Tool	Description	Homepage
topas	This toolkit allows the efficient manipulation of sequence data in various ways. It is organized into modules: The FASTA processing modules, the FASTQ processing modules, the GFF processing modules and the VCF processing modules.	https://github.com/subwaystation/TOPAS

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:49:58 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Ftopas%2Fgencons/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/topas/gencons/blobs/sha256:c693957c94255d3e31243769c71f92c79c0b16ece28addc883a796b659dc4eab
Size	3.9 KB
Checksum	sha256:c693957c94255d3e31243769c71f92c79c0b16ece28addc883a796b659dc4eab