modules/controlfreec_freec

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

cnacnvsomaticsingletumor-only

https://github.com/nf-core/modules/[...]/modules/nf-core/controlfreec/freec

Description

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

Input

name:type

description

pattern

`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

name:type

description

pattern

`bedgraph`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`*_ratio.BedGraph`
`:file`

Bedgraph format for the UCSC genome browser

.bedgraph

`control_cpn`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`*_control.cpn`
`:file`

files with raw copy number profiles

*_control.cpn

`sample_cpn`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`*_sample.cpn`
`:file`

files with raw copy number profiles

*_sample.cpn

`gcprofile_cpn`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`GC_profile.*.cpn`
`:file`

file with GC-content profile.

GC_profile.*.cpn

`BAF`

`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

`CNV`

`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

`info`

`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

`ratio`

`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

`config`

`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

`versions_controlfreec`

`${task.process}`
`:string`

The name of the process

`controlfreec`
`:string`

The name of the tool

`11.6b`
`:string`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`controlfreec`
`:string`

The name of the tool

`11.6b`
`:string`

The expression to obtain the version of the tool

Tools

controlfreec/freec
GPL >=2

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

http://boevalab.inf.ethz.ch/FREEC http://boevalab.inf.ethz.ch/FREEC/tutorial https://github.com/BoevaLab/FREEC/ 10.1093/bioinformatics/btq635

modules/controlfreec_freec

Description

Input

meta:map

mpileup_normal:file

mpileup_tumor:file

cpn_normal:file

cpn_tumor:file

minipileup_normal:file

minipileup_tumor:file

fasta:file

fai:file

snp_position:file

known_snps:file

known_snps_tbi:file

chr_directory:file

mappability:file

target_bed:file

gccontent_profile:file

Output

bedgraph

meta:map

*_ratio.BedGraph:file

control_cpn

meta:map

*_control.cpn:file

sample_cpn

meta:map

*_sample.cpn:file

gcprofile_cpn

meta:map

GC_profile.*.cpn:file

BAF

meta:map

*_BAF.txt:file

CNV

meta:map

*_CNVs:file

info

meta:map

*_info.txt:file

ratio

meta:map

*_ratio.txt:file

config

meta:map

config.txt:file

versions_controlfreec

${task.process}:string

controlfreec:string

11.6b:string

Topics

versions

${task.process}:string

controlfreec:string

11.6b:string

Tools

controlfreec/freec GPL >=2

included in

maintainer

get in touch

`meta`
`:map`

`mpileup_normal`
`:file`

`mpileup_tumor`
`:file`

`cpn_normal`
`:file`

`cpn_tumor`
`:file`

`minipileup_normal`
`:file`

`minipileup_tumor`
`:file`

`fasta`
`:file`

`fai`
`:file`

`snp_position`
`:file`

`known_snps`
`:file`

`known_snps_tbi`
`:file`

`chr_directory`
`:file`

`mappability`
`:file`

`target_bed`
`:file`

`gccontent_profile`
`:file`

`bedgraph`

`meta`
`:map`

`*_ratio.BedGraph`
`:file`

`control_cpn`

`meta`
`:map`

`*_control.cpn`
`:file`

`sample_cpn`

`meta`
`:map`

`*_sample.cpn`
`:file`

`gcprofile_cpn`

`meta`
`:map`

`GC_profile.*.cpn`
`:file`

`BAF`

`meta`
`:map`

`*_BAF.txt`
`:file`

`CNV`

`meta`
`:map`

`*_CNVs`
`:file`

`info`

`meta`
`:map`

`*_info.txt`
`:file`

`ratio`

`meta`
`:map`

`*_ratio.txt`
`:file`

`config`

`meta`
`:map`

`config.txt`
`:file`

`versions_controlfreec`

`${task.process}`
`:string`

`controlfreec`
`:string`

`11.6b`
`:string`

`versions`

`${task.process}`
`:string`

`controlfreec`
`:string`

`11.6b`
`:string`

controlfreec/freec
GPL >=2