Nextflow Registry | nf-core/manta/convertinversion@0.0.0-0c7146d

nf-core/manta/convertinversion @ 0.0.0-0c7146d

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: 0.0.0-0c7146d

Total downloads: 1

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	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:53:50 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fmanta%2Fconvertinversion/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/manta/convertinversion/blobs/sha256:8a8c1c4257679cc64087faac5deb838215d149022ba82f8691eb5ad1fbc85bcb
Size	3.0 KB
Checksum	sha256:8a8c1c4257679cc64087faac5deb838215d149022ba82f8691eb5ad1fbc85bcb
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:53:50 (UTC)		1	3.0 KB	-