modules/manta_convertinversion

Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. This script reformats inversions into single inverted sequence junctions which was the format used in Manta versions <= 1.4.0.

structural variantsconversionindels

https://github.com/nf-core/modules/[...]/modules/nf-core/manta/convertinversion

Description

Input

name:type

description

pattern

`meta`
`:map`

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

`vcf`
`:file`

VCF file produces by Manta

*.vcf.gz

`meta2`
`:map`

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

`fasta`
`:file`

The reference fasta file

*.{fasta,fa,fna}

Output

name:type

description

pattern

`vcf`

`meta`
`:map`

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

`*.vcf.gz`
`:file`

VCF file with reformatted inversions

*.vcf.gz

`tbi`

`meta`
`:map`

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

`*.vcf.gz.tbi`
`:file`

TBI file produces by Manta

*.vcf.gz.tbi

`versions_manta`

`${task.process}`
`:string`

The name of the process

`manta`
`:string`

The name of the tool

`configManta.py --version`
`:eval`

The expression to obtain the version of the tool

`versions_samtools`

`${task.process}`
`:string`

The name of the process

`samtools`
`:string`

The name of the tool

`samtools --version | head -1 | sed -e s'/samtools //'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`manta`
`:string`

The name of the tool

`configManta.py --version`
`:eval`

The expression to obtain the version of the tool

`${task.process}`
`:string`

The name of the process

`samtools`
`:string`

The name of the tool

`samtools --version | head -1 | sed -e s'/samtools //'`
`:eval`

The expression to obtain the version of the tool

Tools

manta
GPL v3

Structural variant and indel caller for mapped sequencing data

github.com/Illumina/manta github.com/Illumina/manta/blob/v1.6.0/docs/userGuide/README.md https://github.com/Illumina/manta 10.1093/bioinformatics/btv710

modules/manta_convertinversion

Description

Input

`meta`
`:map`

`vcf`
`:file`

`meta2`
`:map`

`fasta`
`:file`

Output

`vcf`

`meta`
`:map`

`*.vcf.gz`
`:file`

`tbi`

`meta`
`:map`

`*.vcf.gz.tbi`
`:file`

`versions_manta`

`${task.process}`
`:string`

`manta`
`:string`

`configManta.py --version`
`:eval`

`versions_samtools`

`${task.process}`
`:string`

`samtools`
`:string`

`samtools --version | head -1 | sed -e s'/samtools //'`
`:eval`

Topics

`versions`

`${task.process}`
`:string`

`manta`
`:string`

`configManta.py --version`
`:eval`

`${task.process}`
`:string`

`samtools`
`:string`

`samtools --version | head -1 | sed -e s'/samtools //'`
`:eval`

Tools

manta
GPL v3

maintainer

get in touch

modules/manta_convertinversion

Description

Input

meta:map

vcf:file

meta2:map

fasta:file

Output

vcf

meta:map

*.vcf.gz:file

tbi

meta:map

*.vcf.gz.tbi:file

versions_manta

${task.process}:string

manta:string

configManta.py --version:eval

versions_samtools

${task.process}:string

samtools:string

samtools --version | head -1 | sed -e s'/samtools //':eval

Topics

versions

${task.process}:string

manta:string

configManta.py --version:eval

${task.process}:string

samtools:string

samtools --version | head -1 | sed -e s'/samtools //':eval

Tools

manta GPL v3

maintainer

get in touch

`meta`
`:map`

`vcf`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`vcf`

`meta`
`:map`

`*.vcf.gz`
`:file`

`tbi`

`meta`
`:map`

`*.vcf.gz.tbi`
`:file`

`versions_manta`

`${task.process}`
`:string`

`manta`
`:string`

`configManta.py --version`
`:eval`

`versions_samtools`

`${task.process}`
`:string`

`samtools`
`:string`

`samtools --version | head -1 | sed -e s'/samtools //'`
`:eval`

`versions`

`${task.process}`
`:string`

`manta`
`:string`

`configManta.py --version`
`:eval`

`${task.process}`
`:string`

`samtools`
`:string`

`samtools --version | head -1 | sed -e s'/samtools //'`
`:eval`

manta
GPL v3