Nextflow Registry | nf-core/controlfreec/freec@0.0.0-6c4ed3a

nf-core/controlfreec/freec @ 0.0.0-6c4ed3a

Copy number and genotype annotation from whole genome and whole exome sequencing data

cna cnv somatic single tumor-only

Latest version: 0.0.0-6c4ed3a

Total downloads: 10

Source: nf-core/modules

Authors: @FriederikeHanssen

Maintainers: @FriederikeHanssen

Copy number and genotype annotation from whole genome and whole exome sequencing data

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

include { CONTROLFREEC_FREEC } from 'nf-core/controlfreec/freec'

MIT License

Process

`Name`	`CONTROLFREEC_FREEC`

Input 10 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`mpileup_normal` file	miniPileup file
`mpileup_tumor` file	miniPileup file
`cpn_normal` file	Raw copy number profiles (optional) `*.cpn`
`cpn_tumor` file	Raw copy number profiles (optional) `*.cpn`
`minipileup_normal` file	miniPileup file from previous run (optional) `*.pileup`
`minipileup_tumor` file	miniPileup file from previous run (optional) `*.pileup`

`fasta` file	Reference file (optional; required if args 'makePileup' is set) `*.{fasta,fna,fa}`

`fai` file	Fasta index `*.fai`

`snp_position` file	Path to a BED or VCF file with SNP positions to create a mini pileup file from the initial BAM file provided in mateFile (optional) `*.{bed,vcf}`

`known_snps` file	File with known SNPs `*.{vcf,vcf.gz}`

`known_snps_tbi` file	Index of known_snps `*.tbi`

`chr_directory` file	Path to directory with chromosome fasta files (optional, required if gccontentprofile is not provided) `*/`

`mappability` file	Contains information of mappable positions (optional) `*.gem`

`target_bed` file	Sorted bed file containing capture regions (optional) `*.bed`

`gccontent_profile` file	File with GC-content profile

Output 10 channels

#1 BAF tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*_BAF.txt` file	file B-allele frequencies for each possibly heterozygous SNP position `*_BAF.txt`

#2 CNV tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*_CNVs` file	file with coordinates of predicted copy number alterations. `*_CNVs`

#3 info tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*_info.txt` file	parsable file with information about FREEC run `*_info.txt`

#4 ratio tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*_ratio.txt` file	file with ratios and predicted copy number alterations for each window `*_ratio.txt`

#5 config tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`config.txt` file	Config file used to run Control-FREEC `config.txt`