modules/topas_gencons

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

consensusfastaancient DNA

https://github.com/nf-core/modules/[...]/modules/nf-core/topas/gencons

Description

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

Input

name:type

description

pattern

`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

`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

`meta3`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`reference`
`:file`

Fasta file of reference genome

*.fasta

`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

name:type

description

pattern

`fasta`

`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

`vcf`

`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

`ccf`

`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

`log`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`*.log`
`:file`

Log file

*.log

`versions`

`versions.yml`
`:file`

File containing software versions

versions.yml

Tools

topas
CC-BY

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.

github.com/subwaystation/TOPAS github.com/subwaystation/TOPAS/wiki/Overview-Modules https://github.com/subwaystation/TOPAS 10.1038/s41598-017-17723-1

modules/topas_gencons

Description

Input

`meta`
`:map`

`vcf`
`:file`

`meta2`
`:map`

`vcf_indels`
`:file`

`meta3`
`:map`

`reference`
`:file`

`meta4`
`:map`

`fai`
`:file`

`vcf_output`
`:boolean`

Output

`fasta`

`meta`
`:map`

`*.fasta.gz`
`:file`

`vcf`

`meta`
`:map`

`*.vcf.gz`
`:file`

`ccf`

`meta`
`:map`

`*.ccf`
`:file`

`log`

`meta`
`:map`

`*.log`
`:file`

`versions`

`versions.yml`
`:file`

Tools

topas
CC-BY

maintainer

get in touch

modules/topas_gencons

Description

Input

meta:map

vcf:file

meta2:map

vcf_indels:file

meta3:map

reference:file

meta4:map

fai:file

vcf_output:boolean

Output

fasta

meta:map

*.fasta.gz:file

vcf

meta:map

*.vcf.gz:file

ccf

meta:map

*.ccf:file

log

meta:map

*.log:file

versions

versions.yml:file

Tools

topas CC-BY

maintainer

get in touch

`meta`
`:map`

`vcf`
`:file`

`meta2`
`:map`

`vcf_indels`
`:file`

`meta3`
`:map`

`reference`
`:file`

`meta4`
`:map`

`fai`
`:file`

`vcf_output`
`:boolean`

`fasta`

`meta`
`:map`

`*.fasta.gz`
`:file`

`vcf`

`meta`
`:map`

`*.vcf.gz`
`:file`

`ccf`

`meta`
`:map`

`*.ccf`
`:file`

`log`

`meta`
`:map`

`*.log`
`:file`

`versions`

`versions.yml`
`:file`

topas
CC-BY