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c189835b1b
* 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
183 lines
5.7 KiB
YAML
183 lines
5.7 KiB
YAML
name: controlfreec
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description: Copy number and genotype annotation from whole genome and whole exome sequencing data
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keywords:
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- cna
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- cnv
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- somatic
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- single
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- tumor-only
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tools:
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- controlfreec:
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description: Copy number and genotype annotation from whole genome and whole exome sequencing data.
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homepage: http://boevalab.inf.ethz.ch/FREEC
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documentation: http://boevalab.inf.ethz.ch/FREEC/tutorial.html
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tool_dev_url: https://github.com/BoevaLab/FREEC/
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doi: "10.1093/bioinformatics/btq635"
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licence: ['GPL >=2']
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input:
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- args:
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type: map
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description: |
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Groovy Map containing tool parameters. MUST follow the structure/keywords below and be provided via modules.config.
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<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:
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For default values, please check the documentation above.
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```
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{
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[
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"general" :[
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"bedgraphoutput": <optional>,
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"breakpointthreshold": <optional>,
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"breakpointtype": <optional>,
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"coefficientofvariation": <optional>,
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"contamination": <optional>,
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"contaminationadjustment": <optional>,
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"degree": <optional>,
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"forcegccontentnormalization": <optional>,
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"gccontentprofile": <optional>,
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"intercept": <optional>,
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"mincnalength": <optional>,
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"minmappabilityperwindow": <optional>,
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"minexpectedgc": <optional>,
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"maxexpectedgc": <optional>,
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"minimalsubclonepresence": <optional>,
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"noisydata": <optional>,
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"ploidy": <optional>,
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"printNA": <optional>,
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"readcountthreshold": <optional >,
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"sex": <optional>,
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"step": <optional value>,
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"telocentromeric": <optional>,
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"uniquematch": <optional>,
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"window": <optional>
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],
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"control":[
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"inputformat": <required>,
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"mateorientation": <optional>,
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],
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"sample":[
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"inputformat": <required>,
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"mateorientation": <optional>,
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],
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"BAF":[
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"minimalcoverageperposition": <optional>,
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"minimalqualityperposition": <optional>,
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"shiftinquality": <optional>
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]
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]
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}
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```
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- mateFile_normal:
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type: file
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description: File with mapped reads
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pattern: "*.{sam,bam,pileup(.gz),bowtie(.gz),eland(.gz),arachne(.gz),psl(.gz),bed(.gz)}"
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- mateFile_tumor:
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type: file
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description: File with mapped reads
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pattern: "*.{sam,bam,pileup(.gz),bowtie(.gz),eland(.gz),arachne(.gz),psl(.gz),bed(.gz)}"
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- cpn_normal:
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type: file
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description: Raw copy number profiles (optional)
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pattern: "*.cpn"
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- cpn_tumor:
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type: file
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description: Raw copy number profiles (optional)
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pattern: "*.cpn"
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- minipileup_normal:
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type: file
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description: miniPileup file from previous run (optional)
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pattern: "*.pileup"
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- minipileup_tumor:
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type: file
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description: miniPileup file from previous run (optional)
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pattern: "*.pileup"
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- fasta:
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type: file
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description: Reference file (optional; required if args 'makePileup' is set)
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pattern: "*.{fasta,fna,fa}"
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- fai:
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type: file
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description: Fasta index
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pattern: "*.fai"
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- snp_position:
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type: file
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description:
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pattern: "*.{}"
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- known_snps:
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type: file
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description: File with known SNPs
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pattern: "*.{vcf,vcf.gz}"
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- known_snps_tbi:
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type: file
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description: Index of known_snps
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pattern: "*.tbi"
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- chr_directory:
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type: file
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description: Path to directory with chromosome fasta files (optional, required if gccontentprofile is not provided)
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pattern: "*/"
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- mappability:
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type: file
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description: Contains information of mappable positions (optional)
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pattern: "*.gem"
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- target_bed:
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type: file
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description: Sorted bed file containing capture regions (optional)
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pattern: "*.bed"
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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- bedgraph:
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type: file
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description: Bedgraph format for the UCSC genome browser
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pattern: ".bedgraph"
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- control_cpn:
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type: file
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description: files with raw copy number profiles
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pattern: "*_control.cpn"
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- sample_cpn:
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type: file
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description: files with raw copy number profiles
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pattern: "*_sample.cpn"
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- gcprofile_cpn:
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type: file
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description: file with GC-content profile.
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pattern: "GC_profile.*.cpn"
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- BAF:
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type: file
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description: file B-allele frequencies for each possibly heterozygous SNP position
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pattern: "*_BAF.txt"
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- CNV:
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type: file
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description: file with coordinates of predicted copy number alterations.
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pattern: "*_CNVs"
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- info:
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type: file
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description: parsable file with information about FREEC run
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pattern: "*_info.txt"
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- ratio:
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type: file
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description: file with ratios and predicted copy number alterations for each window
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pattern: "*_ratio.txt"
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- config:
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type: file
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description: Config file used to run Control-FREEC
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pattern: "config.txt"
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authors:
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- "@FriederikeHanssen"
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