nf-core/raredisease
Call and score variants from WGS/WES of rare disease patients.
Define where the pipeline should find input data and save output data.
Path to comma-separated file containing information about the samples in the experiment.
string^\S+\.csv$You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See usage docs.
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringresultsEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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.
MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringReference genome related files and options required for the workflow.
The amount to pad each end of the target intervals to create bait intervals.
integer100^\S+\.bed(\.gz)?$Directory for pre-built bwa index.
stringIf none provided, will be generated automatically from the FASTA reference.
Directory for pre-built bwamem2 index.
stringIf none provided, will be generated automatically from the FASTA reference.
Path to the directory containing cadd annotations.
stringThis folder contains the uncompressed files that would otherwise be in data/annotation folder as described in https://github.com/kircherlab/CADD-scripts/#manual-installation.
Path to FASTA genome index file.
string^\S+\.fn?a(sta)?\.fai$If none provided, will be generated automatically from the FASTA reference
Path to FASTA genome file.
string^\S+\.fn?a(sta)?(\.gz)?$This parameter is mandatory if --genome is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with --save_reference to save BWA index for future runs.
A file containing the path to models produced by GATK4 GermlineCNVCaller cohort.
stringThis model is required for generating a cnv calls when using GermlineCNVCaller.
Name of iGenomes reference.
stringIf using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. --genome GRCh38.
See the nf-core website docs for more details.
Path to a list of common SNP locations for Gens.
stringLocations of gnomad SNPs with a high enough BAF.
Path to interval list for Gens.
stringThis file contains the binning intervals used for CollectReadCounts.
Path to female panel of normals for Gens.
stringThe female panel used to run DenoiseReadCounts.
Path to male panel of normals for Gens.
stringThe male panel used to run DenoiseReadCounts.
Path to the gnomad tab file with allele frequencies.
string^\S+\.tab(\.gz)?$Path to the gnomad tab file with CHR/START/REF,ALT/AF. Can be generated from the gnomad annotations vcf.
Path to the index file for the gnomad tab file with allele frequencies.
string^\S+\.bed(\.gz)?\.idx$Path to the index of gnomad tab file with CHR/START/REF,ALT/AF
Do not load the iGenomes reference config.
booleanDo not load igenomes.config when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in igenomes.config.
Path to the interval list of the genome (autosomes, sex chromosomes, and mitochondria).
string^\S+\.intervals?(_list)?$Path to the interval list of the genome. This is used to calculate genome-wide coverage statistics.
Path to the interval list of the Y chromosome.
string^\S+\.intervals?(_list)?$Path to the interval list of the Y chromosome. This is used to calculate coverage statistics for the Y chromosome.
Path to known dbSNP file.
string^\S+\.vcf(\.gz)?$Path to known dbSNP file index.
string^\S+\.vcf(\.gz)?\.tbi$Local directory base for genome references that map to the config.
stringThis folder is a flat structure with file names that map to the config.
Name of the mitochondrial contig in the reference fasta file
stringchrMUsed to extract relevant information from the references to analyse mitochondria
File with mobile element references
string^\S+\.tsv$Path to tsv file listing mobile element references.
Format: <mobile element type>\t<path to bed file>
File with mobile element allele frequency references
string^\S+\.csv$Path to csv file listing files containing mobile element allele frequencies in reference populations.
Format: <vcf file path>,<in_freq_info_key>,<in_allele_count_info_key>,<out_freq_info_key>,<out_allele_count_info_key>
Path to sentieon machine learning model file.
stringPath to mitochondrial FASTA genome file.
string^\S+\.fn?a(sta)?(\.gz)?$Directory containing the ploidy model files
stringProduced in GATK4 DetermineGermlineContigPloidy cohort, this model is required for generating a cnv model when using GermlineCNVCaller.
Interval list file containing the intervals over which read counts are tabulated for CNV calling
stringGenerated by GATK4 preprocessintervals. If absent, pipeline can generate this file.
File with gene ids that have reduced penetrance. For use with genmod
stringVcf used for evaluating variant calls.
string^\S+\.csv$Path to comma-separated file containing information about the truth vcf files used by vcfeval.
If generated by the pipeline save the required indices/references in the results directory.
booleanThe saved references can be used for future pipeline runs, reducing processing times.
MT rank model config file for genmod.
stringSNV rank model config file for genmod.
stringSV rank model config file for genmod.
stringDirectory for pre-built sdf index. Used by rtg/vcfeval
stringIf none provided, will be generated automatically from the FASTA reference.
Path to the genome dictionary file
string^\S+\.dict$Databases used for structural variant annotation in chrA-posA-chrB-posB-type-count-frequency format.
string^\S+\.csv$Path to comma-separated file containing information about the databases used for structural variant annotation.
Databases used for structural variant annotation in vcf format.
string^\S+\.csv$Path to comma-separated file containing information about the databases used for structural variant annotation.
Path to directory for target bed file.
string^\S+\.bed(\.gz)?$If you would like to limit your analysis to specific regions of the genome, you can pass those regions in a bed file using this option
Path to variant catalog file
stringShould be Stranger's extended JSON as described at https://github.com/Clinical-Genomics/stranger/blob/master/stranger/resources/variant_catalog_grch37.json. This file is used by both ExpansionHunter and Stranger
Path to a file containing internal ids and customer ids in csv format.
string^\S+\.csv$Optional file to rename sample ids in the vcf2cytosure vcf
Path to vcf2cytosure blacklist file
string^\S+\.bed$Optional file to blacklist regions for VCF2cytosure
Path to a file containing the absolute paths to resources defined within the vcfanno toml file. One line per resource.
stringIf no file is passed, default configurations will be used according to genome build within the context of the pipeline.
Path to the vcfanno toml file.
string^\S+\.toml$If no toml is passed, default configurations will be used according to genome build within the context of the pipeline.
Path to the vcfanno lua file.
string^\S+\.lua$Custom operations file (lua). For use when the built-in ops don't supply the needed reduction.
Path to vep's cache directory.
stringIf no directory path is passed, vcf files will not be annotated by vep.
Databases used by both named and custom plugins to annotate variants.
string^\S+\.csv$Path to a file containing the absolute paths to databases and their indices used by VEP's custom and named plugins resources defined within the vcfanno toml file. One line per resource.
Path to the file containing HGNC_IDs of interest on separate lines.
stringPath to a bed-like file exported by scout, which contains HGNC_IDs to be used in filter_vep.
stringOptions used to steer the direction of the pipeline.
Specifies which analysis type for the pipeline- either 'wgs','wes','mito'. This changes resources consumed and tools used.
stringSpecifies which analysis type for the pipeline- either 'wgs','wes','mito'. This changes resources consumed and tools used.
stringMethod selection for ngs-bits samplegender
stringSpecifies whether to run rtgtools' vcfeval
booleanSpecifies whether to generate and publish alignment files as cram instead of bam
booleanSpecifies whether or not to skip FASTQC.
booleanSpecifies whether or not to skip trimming with fastp.
booleanSpecifies whether or not to skip haplocheck.
booleanSpecifies whether or not to skip gens preprocessing subworkflow.
booleanSpecifies whether or not to skip CNV calling using GATK's GermlineCNVCaller
booleanSpecifies whether or not to skip eKLIPse.
booleanSpecifies whether or not to skip peddy.
booleanSpecifies whether or not to skip Qualimap.
booleanSpecifies whether or not to skip annotation of mobile_elements.
booleanSpecifies whether or not to skip annotation of mitochondrial variants.
booleanSpecifies whether or not to subsample mt alignment.
booleanSpecifies whether or not to skip annotate SNV subworkflow.
booleanSpecifies whether or not to skip annotate structural variant subworkflow.
booleanSpecifies whether or not to skip the vcf2cytosure subworkflow
booleantruevcf2cytosure can generate CGH files from a structural variant VCF file that can be analysed in the CytoSure interpretation software. Cut-offs for allele frequencies and bin sizes can be modified in the config file. Turned off by default.
Specifies whether or not to filter results based on a list of candidate genes specified in 'vep_filters'.
booleanOptions to adjust parameters and filtering criteria for read alignments.
Specifies the alignment algorithm to use - available options are 'bwamem2' and 'sentieon'.
stringDiscard trimmed reads shorter than the given value
integer40Minimum length of reads after adapter trimming. Shorter reads are discarded.
Expected coverage to subsample mt alignment to.
integer150To know more about this parameter check samtools' view documentation.
Subsampling seed used to influence which subset of mitochondrial reads is kept.
integer30To know more about this parameter check samtools' view documentation.
Specifies whether duplicates reads should be removed prior to variant calling.
booleanOptions to adjust parameters and filtering criteria for variant calling.
Interval in the reference that will be used in the software
stringBin size for CNVnator
integer1000Option for selecting the PCR indel model used by Sentieon Dnascope.
stringPCR indel model used to weed out false positive indels more or less aggressively. The possible MODELs are: NONE (used for PCR free samples), and HOSTILE, AGGRESSIVE and CONSERVATIVE, in order of decreasing aggressiveness. The default value is CONSERVATIVE.
Specifies the variant caller to use - available options are 'deepvariant' and 'sentieon'.
stringSpecifies the variant types for sentieon variant caller.
stringOptions used to facilitate the annotation of the variants.
File containing list of SO terms listed in the order of severity from most severe to lease severe for annotating genomic and mitochondrial SNVs.
stringFor more information check https://grch37.ensembl.org/info/genome/variation/prediction/predicted_data.html
File containing list of SO terms listed in the order of severity from most severe to lease severe for annotating genomic SVs.
stringFor more information check https://grch37.ensembl.org/info/genome/variation/prediction/predicted_data.html
Specify the version of the VEP cache provided to the --vep_cache option.
integerParameters 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.
stringSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1
Maximum amount of memory that can be requested for any single job.
string128.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. --max_memory '8.GB'
Maximum amount of time that can be requested for any single job.
string240.h^(\d+\.?\s*(s|m|h|d|day)\s*)+$Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. --max_time '2.h'
Less common options for the pipeline, typically set in a config file.
Display help text.
booleanDisplay 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})$An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.
Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Do not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringIncoming hook URL for messaging service. Currently, MS Teams and Slack are supported.
Custom config file to supply to MultiQC.
stringCustom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
stringCustom MultiQC yaml file containing HTML including a methods description.
stringBoolean whether to validate parameters against the schema at runtime
booleantrueShow all params when using --help
booleanBy default, parameters set as hidden in the schema are not shown on the command line when a user runs with --help. Specifying this option will tell the pipeline to show all parameters.
Validation of parameters fails when an unrecognised parameter is found.
booleanBy default, when an unrecognised parameter is found, it returns a warinig.
Validation of parameters in lenient more.
booleanAllows string values that are parseable as numbers or booleans. For further information see JSONSchema docs.