nf-core_modules/modules/controlfreec/meta.yml

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name: controlfreec
description: Copy number and genotype annotation from whole genome and whole exome sequencing data
keywords:
- cna
- cnv
- somatic
- single
- tumor-only
tools:
- controlfreec:
description: Copy number and genotype annotation from whole genome and whole exome sequencing data.
homepage: http://boevalab.inf.ethz.ch/FREEC
documentation: http://boevalab.inf.ethz.ch/FREEC/tutorial.html
tool_dev_url: https://github.com/BoevaLab/FREEC/
doi: "10.1093/bioinformatics/btq635"
licence: ["GPL >=2"]
input:
- args:
type: map
description: |
Groovy Map containing tool parameters. MUST follow the structure/keywords below and be provided via modules.config.
Parameters marked as (optional) can be removed from the map, if they are not set. All values must be surrounded by quotes, meta map parameters can be set with, i.e. `sex = meta.sex`:
For default values, please check the documentation above.
```
{
[
"general" :[
"bedgraphoutput": (optional),
"breakpointthreshold": (optional),
"breakpointtype": (optional),
"coefficientofvariation": (optional),
"contamination": (optional),
"contaminationadjustment": (optional),
"degree": (optional),
"forcegccontentnormalization": (optional),
"gccontentprofile": (optional),
"intercept": (optional),
"mincnalength": (optional),
"minmappabilityperwindow": (optional),
"minexpectedgc": (optional),
"maxexpectedgc": (optional),
"minimalsubclonepresence": (optional),
"noisydata": (optional),
"ploidy": (optional),
"printNA": (optional),
"readcountthreshold": (optional),
"sex": (optional),
"step": (optional),
"telocentromeric": (optional),
"uniquematch": (optional),
"window": (optional)
],
"control":[
"inputformat": (required),
"mateorientation": (optional),
],
"sample":[
"inputformat": (required),
"mateorientation": (optional),
],
"BAF":[
"minimalcoverageperposition": (optional),
"minimalqualityperposition": (optional),
"shiftinquality": (optional)
]
]
}
```
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- mateFile_normal:
type: file
description: File with mapped reads
pattern: "*.{sam,bam,pileup(.gz),bowtie(.gz),eland(.gz),arachne(.gz),psl(.gz),bed(.gz)}"
- mateFile_tumor:
type: file
description: File with mapped reads
pattern: "*.{sam,bam,pileup(.gz),bowtie(.gz),eland(.gz),arachne(.gz),psl(.gz),bed(.gz)}"
- cpn_normal:
type: file
description: Raw copy number profiles (optional)
pattern: "*.cpn"
- cpn_tumor:
type: file
description: Raw copy number profiles (optional)
pattern: "*.cpn"
- minipileup_normal:
type: file
description: miniPileup file from previous run (optional)
pattern: "*.pileup"
- minipileup_tumor:
type: file
description: miniPileup file from previous run (optional)
pattern: "*.pileup"
- fasta:
type: file
description: Reference file (optional; required if args 'makePileup' is set)
pattern: "*.{fasta,fna,fa}"
- fai:
type: file
description: Fasta index
pattern: "*.fai"
- snp_position:
type: file
description:
pattern: "*.{}"
- known_snps:
type: file
description: File with known SNPs
pattern: "*.{vcf,vcf.gz}"
- known_snps_tbi:
type: file
description: Index of known_snps
pattern: "*.tbi"
- chr_directory:
type: file
description: Path to directory with chromosome fasta files (optional, required if gccontentprofile is not provided)
pattern: "*/"
- mappability:
type: file
description: Contains information of mappable positions (optional)
pattern: "*.gem"
- target_bed:
type: file
description: Sorted bed file containing capture regions (optional)
pattern: "*.bed"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- bedgraph:
type: file
description: Bedgraph format for the UCSC genome browser
pattern: ".bedgraph"
- control_cpn:
type: file
description: files with raw copy number profiles
pattern: "*_control.cpn"
- sample_cpn:
type: file
description: files with raw copy number profiles
pattern: "*_sample.cpn"
- gcprofile_cpn:
type: file
description: file with GC-content profile.
pattern: "GC_profile.*.cpn"
- BAF:
type: file
description: file B-allele frequencies for each possibly heterozygous SNP position
pattern: "*_BAF.txt"
- CNV:
type: file
description: file with coordinates of predicted copy number alterations.
pattern: "*_CNVs"
- info:
type: file
description: parsable file with information about FREEC run
pattern: "*_info.txt"
- ratio:
type: file
description: file with ratios and predicted copy number alterations for each window
pattern: "*_ratio.txt"
- config:
type: file
description: Config file used to run Control-FREEC
pattern: "config.txt"
authors:
- "@FriederikeHanssen"