nf-core_modules/modules/controlfreec/meta.yml
FriederikeHanssen c189835b1b
add controlfreec (#1333)
* add drafty controlfreec

* get sofatware version

* use maps in map

* update paths to new and soon-to-be merged test files, add more input docu

* Stab at documenting args map

* Update syntax

* Bit more description

* Make the linter happy

* tests pass locally

* Add outputs & docu

* tests are failing locally now :/ but cpn file can also be added

* All tests passing, need to update test data again to add folder

* Clean up files

* Clean up files

* Clean up files

* Don't know how to get the test to run with the direcotry for now. they pass locally though

* Make linter happy

* Name process back

* Update to use tar folder

* fix the checksum
2022-02-28 19:08:58 +01:00

183 lines
5.7 KiB
YAML

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.
<optional> parameters can be removed from the map, if they are not set. All value 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 value>,
"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"