nf-core/raredisease
Call and score variants from WGS/WES of rare disease patients.
2.4.0). The latest
stable release is
2.6.0
.
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$The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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)?$Directory for pre-built bwa index.
stringDirectory for pre-built bwamem2 index.
stringDirectory for pre-built bwameme’s learned index.
stringPath to the directory containing cadd annotations.
stringPath to FASTA genome index file.
string^\S+\.fn?a(sta)?\.fai$Path to FASTA genome file.
string^\S+\.fn?a(sta)?(\.gz)?$A file containing the path to models produced by GATK4 GermlineCNVCaller cohort.
stringName of iGenomes reference.
stringPath to a list of common SNP locations for Gens.
stringPath to interval list for Gens.
stringPath to female panel of normals for Gens.
stringPath to male panel of normals for Gens.
stringPath to the gnomad tab file with allele frequencies.
string^\S+\.tab(\.gz)?$Path to the index file for the gnomad tab file with allele frequencies.
string^\S+\.bed(\.gz)?\.idx$The base path to the igenomes reference files
strings3://ngi-igenomes/igenomes/Do not load the iGenomes reference config.
booleanPath to the interval list of the genome (autosomes, sex chromosomes, and mitochondria).
string^\S+\.intervals?(_list)?$Path to the interval list of the Y chromosome.
string^\S+\.intervals?(_list)?$Path to known dbSNP file.
string^\S+\.vcf(\.gz)?$Path to known dbSNP file index.
string^\S+\.vcf(\.gz)?\.tbi$Local directory base for genome references that map to the config.
stringName of the mitochondrial contig in the reference fasta file
stringchrMFile with mobile element references
string^\S+\.tsv$File with mobile element allele frequency references
string^\S+\.csv$Path to sentieon machine learning model file.
stringPath to mitochondrial FASTA genome file.
string^\S+\.fn?a(sta)?(\.gz)?$Path to a BED file containing PAR regions (used by deepvariant).
string^\S+\.bed(\.gz)?$Directory containing the ploidy model files
stringInterval list file containing the intervals over which read counts are tabulated for CNV calling
stringFile with gene ids that have reduced penetrance. For use with genmod
stringVcf used for evaluating variant calls.
string^\S+\.csv$If generated by the pipeline save the required indices/references in the results directory.
booleanMT 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
stringPath to the genome dictionary file
string^\S+\.dict$Databases used for structural variant annotation in chrA-posA-chrB-posB-type-count-frequency format.
string^\S+\.csv$Databases used for structural variant annotation in vcf format.
string^\S+\.csv$Path to directory for target bed file.
string^\S+\.bed(\.gz)?$Path to variant catalog file
stringPath to a file containing internal ids and customer ids in csv format.
string^\S+\.csv$Path to vcf2cytosure blacklist file
string^\S+\.bed$Path to a VCF file containing annotations.
stringPath to a file containing the absolute paths to resources defined within the vcfanno toml file. One line per resource.
stringPath to the vcfanno toml file.
string^\S+\.toml$Path to the vcfanno lua file.
string^\S+\.lua$Path to vep’s cache directory.
stringDatabases used by both named and custom plugins to annotate variants.
string^\S+\.csv$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’ or ‘mito’. This changes resources consumed and tools used.
stringSpecifies whether or not to use bwa as a fallback aligner in case bwamem2 throws an error.
booleanAfter aligning the reads to a reference, extract alignments from specific regions/contigs and restrict the analysis to those regions/contigs.
booleanfalseSpecifies the platform on which the reads were sequenced.
stringilluminaMethod selection for ngs-bits samplegender
stringCan be specified as RNAME[:STARTPOS]. Multiple regions should be seperated by space
stringSpecifies whether to run mitochondrial analysis for wes samples
booleanSpecifies whether to run rtgtools’ vcfeval
booleanSpecifies whether to generate and publish alignment files as cram instead of bam
booleanNumber of intervals to split your genome into (used to parallelize annotations)
integer20Specifies whether or not to skip trimming with fastp.
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 haplogrep3.
booleanSpecifies whether or not to skip peddy.
booleanSpecifies whether or not to skip calling mobile elements, and the subsequent annotation step.
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 annotation of repeat expansions.
booleanSpecifies whether or not to skip calling of repeat expansions.
booleanSpecifies whether or not to skip smncopynumbercaller.
booleanSpecifies whether or not to skip annotate SNV subworkflow.
booleanSpecifies whether or not to skip nuclear and mitochondrial SNV calling and annotation.
booleanSpecifies whether or not to skip annotate structural variant subworkflow.
booleanSpecifies whether or not to skip nuclear and mitochondrial SV calling and annotation.
booleanSpecifies whether or not to skip the vcf2cytosure subworkflow
booleantrueSpecifies 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’, ‘bwa’, ‘bwameme’ and ‘sentieon’.
stringSpecifies the alignment algorithm to use - available options are ‘bwamem2’, ‘bwa’ and ‘sentieon’.
stringNumber of threads allocated for sorting alignment files (used only by bwameme)
integer4Memory allocated for mbuffer in megabytes (used only by bwameme)
integer3072Discard trimmed reads shorter than the given value
integer40Expected coverage to subsample mt alignment to.
integer150Subsampling seed used to influence which subset of mitochondrial reads is kept.
integer30Specifies 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. Used only by sentieon.
stringBin size for CNVnator
integer1000Option for selecting the PCR indel model used by Sentieon Dnascope.
stringSpecifies 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.
stringFile containing list of SO terms listed in the order of severity from most severe to lease severe for annotating genomic SVs.
stringSpecify the version of the VEP cache provided to the --vep_cache option.
integer112Parameters 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/masterInstitutional 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.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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
stringCustom 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
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