Nextflow Registry | nf-core/manta/convertinversion@0.0.0-6c4ed3a

nf-core/manta/convertinversion @ 0.0.0-6c4ed3a

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 variants conversion indels

Latest version: 0.0.0-6c4ed3a

Total downloads: 6

Source: nf-core/modules

Authors: @FriederikeHanssen

Maintainers: @FriederikeHanssen

Summary

Get started

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

include { MANTA_CONVERTINVERSION } from 'nf-core/manta/convertinversion'

License

MIT License

Process

`Name`	`MANTA_CONVERTINVERSION`

Input 2 channels

#1 tuple

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

#2 tuple

`meta2` map	Groovy Map containing fasta information e.g. [ id:'test', single_end:false ]
`fasta` file	The reference fasta file `*.{fasta,fa,fna}`

Output 4 channels

#1 tbi tuple

`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`

#2 vcf tuple

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

#3 versions_manta tuple

`${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

#4 versions_samtools tuple

`${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

Tool	Description	Homepage
manta	Structural variant and indel caller for mapped sequencing data	https://github.com/Illumina/manta

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:29:22 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fmanta%2Fconvertinversion/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/manta/convertinversion/blobs/sha256:4f8b261e011386a84381eab69eb69d435d6dc692aef3635914f4d3811207eef7
Size	3.1 KB
Checksum	sha256:4f8b261e011386a84381eab69eb69d435d6dc692aef3635914f4d3811207eef7
Downloads	3

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:29:22 (UTC)		3	3.1 KB
0.0.0-0c7146d	08 Apr 2026 19:16:02 (UTC)		3	3.0 KB