Nextflow Registry | nf-core/cnvkit/batch@0.0.0-6c4ed3a

nf-core/cnvkit/batch @ 0.0.0-6c4ed3a

Copy number variant detection from high-throughput sequencing data

cnvkit bam fasta copy number

Latest version: 0.0.0-6c4ed3a

Total downloads: 14

Source: nf-core/modules

Authors: @adamrtalbot @drpatelh @fbdtemme @kaurravneet4123 @KevinMenden @lassefolkersen @MaxUlysse @priesgo @SusiJo

Maintainers: @adamrtalbot @drpatelh @fbdtemme @kaurravneet4123 @KevinMenden @lassefolkersen @MaxUlysse @priesgo @SusiJo

Copy number variant detection from high-throughput sequencing data

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

include { CNVKIT_BATCH } from 'nf-core/cnvkit/batch'

MIT License

Process

`Name`	`CNVKIT_BATCH`

Input 5 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`tumor` file	Input tumour sample bam file (or cram) `*.{bam,cram}`
`tumor_index` file	Input tumour sample bam/cram index file (only needed for bam input) `*.{bai,crai}`
`normal` file	Input normal sample bam file (or cram) `*.{bam,cram}`
`normal_index` file	Input normal sample bam/cram index file (only needed for bam input) `*.{bai,crai}`

#2 tuple

`meta2` map	Groovy Map containing reference information e.g. [ id:'test' ]
`fasta` file	Input reference genome fasta file (only needed for cram_input and/or when normal_samples are provided) `*.{fa,fasta}`
`fasta_fai` file	Input reference genome fasta index (optional, but recommended for cram_input) `*.{fai}`

#3 tuple

`meta4` map	Groovy Map containing information about target file e.g. [ id:'test' ]
`targets` file	Input target bed file `*.{bed}`

#4 tuple

`meta5` map	Groovy Map containing information about reference file e.g. [ id:'test' ]
`reference` file	Input reference cnn-file (only for germline and tumor-only running) `*.{cnn}`

`panel_of_normals` file	Input panel of normals file `*.{cnn}`

Output 8 channels

#1 bed tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.bed` file	File containing genomic regions `*.{bed}`

#2 cnn tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.cnn` file	File containing coverage information `*.{cnn}`

#3 cnr tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.cnr` file	File containing copy number ratio information `*.{cnr}`

#4 cns tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.cns` file	File containing copy number segment information `*.{cns}`

#5 pdf tuple

`*.pdf` file
`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]