Nextflow Registry | nf-core/mitorsaw/haplotype@0.0.0-6c4ed3a

nf-core/mitorsaw/haplotype @ 0.0.0-6c4ed3a

Mitorsaw analyses mitochondrial variants and identifies heteroplasmy and homoplasmy

heteroplasmy homoplasmy mitochondrial mitorsaw haplotype

Latest version: 0.0.0-6c4ed3a

Total downloads: 9

Source: nf-core/modules

Authors: @eliottBo

Maintainers: @eliottBo

Mitorsaw analyses mitochondrial variants and identifies heteroplasmy and homoplasmy

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

include { MITORSAW_HAPLOTYPE } from 'nf-core/mitorsaw/haplotype'

MIT License

Process

`Name`	`MITORSAW_HAPLOTYPE`

Input 4 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`bam` file	Sorted BAM file `*.bam`
`bai` file	BAM index file `*.bai`

#2 tuple

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

`include_hap_stats` boolean	Whether to include haplotype statistics output file

`include_debug_output` boolean	Whether to generate debug output files

Output 12 channels

#1 tbi tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'sample1' ]
`*${prefix}.vcf.gz.tbi` file	Index file for the compressed VCF file `*.vcf.gz.tbi`

#2 vcf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'sample1' ]
`*${prefix}.vcf.gz` file	Compressed VCF file containing haplotype information `*.vcf.gz`

#3 stats tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'sample1' ]
`${prefix}.json` file	Mitorsaw statistics in JSON format `*.json`

#4 igv_session tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'sample1' ]
`${prefix}_debug/mito_igv_custom/custom_igv_session.xml` file	IGV session file in XML format `custom_igv_session.xml`

#5 custom_ref_fa tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'sample1' ]
`${prefix}_debug/mito_igv_custom/custom_reference.fa` file	Custom reference genome in FASTA format `custom_reference.fa`

#6 coverage_stats tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'sample1' ]
`${prefix}_debug/coverage_stats.json` file	Coverage statistics in JSON format `coverage_stats.json`

#7 custom_ref_fai tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'sample1' ]
`${prefix}_debug/mito_igv_custom/custom_reference.fa.fai` file	Custom reference genome index file `custom_reference.fa.fai`

#8 custom_regions tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'sample1' ]
`${prefix}_debug/mito_igv_custom/custom_regions.bed` file	Custom regions in BED format `custom_regions.bed`

#9 sequences_chrM tuple

`meta` map