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

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

Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs.

somatic wgs wxs panel vcf structural variants small indels

Latest version: 0.0.0-6c4ed3a

Total downloads: 6

Source: nf-core/modules

Authors: @maxulysse @ramprasadn @nvnieuwk

Maintainers: @maxulysse @ramprasadn @nvnieuwk

Summary

Get started

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

include { MANTA_GERMLINE } from 'nf-core/manta/germline'

License

MIT License

Process

`Name`	`MANTA_GERMLINE`

Input 4 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`input` file	BAM/CRAM/SAM file. For joint calling use a list of files. `*.{bam,cram,sam}`
`index` file	BAM/CRAM/SAM index file. For joint calling use a list of files. `*.{bai,crai,sai}`
`target_bed` file	BED file containing target regions for variant calling `*.{bed}`
`target_bed_tbi` file	Index for BED file containing target regions for variant calling `*.{bed.tbi}`

#2 tuple

`meta2` map	Groovy Map containing reference information e.g. [ id:'genome' ]
`fasta` file	Genome reference FASTA file `*.{fa,fasta}`

#3 tuple

`meta3` map	Groovy Map containing reference information e.g. [ id:'genome' ]
`fai` file	Genome reference FASTA index file `*.{fa.fai,fasta.fai}`

`config` file	Manta configuration file `*.{ini,conf,config}`

Output 7 channels

#1 diploid_sv_vcf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*diploid_sv.vcf.gz` file	Gzipped VCF file containing variants `*.{vcf.gz}`

#2 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

#3 candidate_sv_vcf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*candidate_sv.vcf.gz` file	Gzipped VCF file containing variants `*.{vcf.gz}`

#4 diploid_sv_vcf_tbi tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*diploid_sv.vcf.gz.tbi` file	Index for gzipped VCF file containing variants `*.{vcf.gz.tbi}`

#5 candidate_sv_vcf_tbi tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*candidate_sv.vcf.gz.tbi` file	Index for gzipped VCF file containing variants `*.{vcf.gz.tbi}`

#6 candidate_small_indels_vcf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*candidate_small_indels.vcf.gz` file	Gzipped VCF file containing variants `*.{vcf.gz}`

#7 candidate_small_indels_vcf_tbi tuple

`meta` map