nf-core/rarevariantburden
Pipeline for performing consistent summary count based rare variant burden test, which is useful when we only have sequenced cases data. For example, we can compare the cases against public summary count data, such as gnomAD.
Define where the pipeline should find input data and save output data.
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (~/.nextflow/config) then you don't need to specify this on the command line for every run.
Define different pipeline parameters.
Joined called and VQSR applied vcf file from the case cohort
stringOne column text file containing list of samples, one sample ID per line.
stringInput files needed for the pipeline from the control dataset, for now we support 3 gnomAD datasets as control, gnomADv2exome, gnomADv4.1exome, gnomADv4.1genome. You need to download these datasets from our Amazon AWS s3 bucket: s3://cocorv-resource-files/
stringResource folder for the annotation tool Annovar, you can download this folder from our Amazon AWS s3 bucket: s3://cocorv-resource-files/
stringResource folder for the annotation tool VEP, you can download this folder from our Amazon AWS s3 bucket: s3://cocorv-resource-files/
stringReference genome build version, allowed values are "GRCh37", "GRCh38". Default value: "GRCh37""
stringGRCh37gnomAD version, allowed values are "v2exome", "v4exome", "v4genome" (for GRCh37 data use "v2exome", for GRCh38, use "v4exome" or "v4genome"). Default value: "v2exome""
stringv2exomeBed file containing good coverage positions from case vcf files where 90% samples have coverage >= 10.
stringNAList of chromosomes you want to analyze, you can test only for chromosome 21 and 22, in that case, it will be "21 22"
string1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22Annotation options for Annovar, default: 'refGene,gnomad211_exome,revel'
stringrefGene,gnomad211_exome,revelAnnotation options for Annovar, default: 'g,f,f'
stringg,f,fIf you want to add VEP annotation, you need to put "T" for this parameter. Default: "F", meaning do not run VEP annotaion, only run Annovar.
stringFVEP annotation parameters
stringAM,SPLICEAI,CADD,LOFTEEAnnotation options for Annovar
stringNAAnnotation options for Annovar
stringNAFile containing estimation of the population/ethnicity of case samples using gnomAD classifier, optional, if not specified nextflow app will estimate the population using gnomAD classifier.
stringNAAn optional R file with functions or a tab separated two column text file defining the variants of interest
stringNAAn optional JASON file to provide extra parameters to the custuomized file variantGroupCustom
stringNAA one column file without the header listing all required annotations used in variant filtering. AC AN annotations from ACANConfig will be added automatically
stringNAOptional options for CoCoRV module
stringNAThe column header used to pull Gene name from annotation file
stringGene.refGeneA one column file specifying the variants to be included, it will also include variants specified in variantExcludeFile
stringNABatch size for CoCoRV module
integer10000The folder path containing CoCoRV R package
string/opt/cocorv/The maximum of the alternate allele frequency, for gnomADv2exome, we used 0.0001, for gnomADv4.1genome and v4.1exome, we used 0.0005
number0.0001The maximum missingness allowed for a variant
number0.1A specified variant group to use for test or a self defined function to define the variants of interest
stringannovar_pathogenicThe minimum REVEL score for pathogenic missense variants
number0.65The p-value threshold to detect high LD variants in control
number0.05Top K genes for generating variant-sample list
integer20Case or control for which top K genes need to be examined
stringcaseBed file containing good coverage positions from gnomAD control files where 90% samples have coverage >= 10.
stringnull/coverage10x.bed.gzThe files containing variant positions needed for gnomAD ancestry prediction classifier
stringnull/ancestry/hail_positions.chr.pos.tsvFiles needed for gnomAD ancestry prediction classifier
stringnull/ancestry/gnomad.pca_loadings.ht/Files needed for gnomAD ancestry prediction classifier
stringnull/ancestry/gnomad.RF_fit.onnxThe reference genome file
stringnull/reference.fasta.gzIf you split you joined called VCF file by chromosome, you can supply the VCF file list here, the list needs to be in csv format (comma seperated), the column headers are chr,vcf. Then you need to list the chromosome number and the coresponding vcf file for that chromosome.
stringNAPre-annotated case VCF files, you can use the pre-annotated case VCF files to skip the annotation steps in the pipeline, the list needs to be in csv format (comma seperated), the column headers are chr,vcf. Then you need to list the chromosome number and the coresponding vcf file for that chromosome.
stringNAGDS converted genotype case VCF files, you can use it to skip the genotype GDS conversion steps in the pipeline, the list needs to be in csv format (comma seperated), the column headers are chr,gds. Then you need to list the chromosome number and the coresponding gds file for that chromosome.
stringNAGDS converted annotated case VCF files, you can use it to skip the annotation GDS conversion steps in the pipeline, the list needs to be in csv format (comma seperated), the column headers are chr,gds. Then you need to list the chromosome number and the coresponding vcf file for that chromosome.
stringNAGDS converted genotype control VCF files
stringnull/controlGenotypeGDS.csvGDS converted annotated control VCF files
stringnull/controlAnnotationGDS.csvParameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterIf you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.
Institutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringLess common options for the pipeline, typically set in a config file.
Display version and exit.
booleanMethod used to save pipeline results to output directory.
stringThe Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.
Email address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.
Send plain-text email instead of HTML.
booleanDo not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringIncoming hook URL for messaging service. Currently, MS Teams and Slack are supported.
Boolean whether to validate parameters against the schema at runtime
booleantrueBase URL or local path to location of pipeline test dataset files
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.
string