nf-core/raredisease
Call and score variants from WGS/WES of rare disease patients.
1.0.0). 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.
number100^\S+\.bed(\.gz)?$Name of iGenomes reference.
stringPath to FASTA genome file.
string^\S+\.fn?a(sta)?(\.gz)?$Path to FASTA genome index file.
string^\S+\.fn?a(sta)?\.fai$Directory / URL base for iGenomes references.
strings3://ngi-igenomes/igenomesDo not load the iGenomes reference config.
booleanDirectory for pre-built bwa index.
stringDirectory for pre-built bwamem2 index.
stringPath to the gnomad tab file with allele frequencies.
string^\S+\.tab(\.gz)?$Path to the index file for the gnomad tab file with allele frequencies.
string^\S+\.bed(\.gz)?\.idx$Path to the interval list of the genome (autosomes, sex chromosomes, and mitochondria).
string^\S+\.intervals?(_list)?$Path to the interval list of the Y chromosome.
string^\S+\.intervals?(_list)?$Name of the mitochondrial contig in the reference fasta file
stringPath to the interval list of the non control mitochondral region.
string^\S+\.intervals?(_list)?$Path to the interval list of the non control mitochondral region in shifted fasta.
string^\S+\.intervals?(\_list)?$Path to known dbSNP file.
string^\S+\.vcf(\.gz)?$Path to known dbSNP file index.
string^\S+\.vcf(\.gz)?\.tbi$Path to known indels file.
string^\S+\.vcf(\.gz)?$Path to known Mills file.
string^\S+\.vcf(\.gz)?$Path to sentieon machine learning model file.
stringPath to mitochondrial FASTA genome file.
string^\S+\.fn?a(sta)?(\.gz)?$Path to mitochondrial FASTA genome index file.
string^\S+\.fn?a(sta)?\.fai?$Directory for pre-built bwa index for shifted mitochondrial fasta (used for alignment with sentioen)
stringDirectory for pre-built bwamem2 index for shifted mitochondrial fasta.
stringChain file describing the alignment between the mitochondrial shifted fasta and typical mitochondrial fasta
stringFile with gene ids that have reduced penetrance. For use with genmod
stringSNV rank model config file for genmod.
stringSV rank model config file for genmod.
stringGenome dictionary file
string^\S+\.dict$Shifted mitochondrial genome dictionary file
string^\S+\.dict$File containing HGNC_IDs of interest on separate lines.
stringPath to directory for target bed file.
string^\S+\.bed(\.gz)?$Databases used for structural variant annotation.
stringPath to variant catalog file
stringText 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.
stringIf generated by the pipeline save the required indices/references in the results directory.
booleanLocal directory base for genome references that map to the config.
stringPath to interval list for Gens.
stringPath to panel of normals for Gens.
stringPath to a list of common SNP locations for Gens.
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 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 subworkflow that analyses mitochondrial genome separate from the nuclear genome.
booleanSpecifies whether or not to run gens preprocessing subworkflow.
booleanSpecifies which analysis type for the pipeline- either ‘wgs’,‘wes’,‘mito’. This changes resources consumed and tools used.
stringOptions to adjust parameters and filtering criteria for read alignments.
Specifies the alignment algorithm to use - available options are ‘bwamem2’ and ‘sentieon’.
stringSpecifies 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
stringIndicates whether the sample library is amplified using PCR or not. Set to false for PCR Free samples.
booleanSpecifies the variant types for sentieon variant caller.
stringSpecifies the variant caller to use - available options are ‘deepvariant’ and ‘sentieon’.
stringOptions used to facilitate the annotation of the variants.
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/masterInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringPath to local config
stringSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Maximum amount of memory that can be requested for any single job.
string128.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Maximum amount of time that can be requested for any single job.
string240.h^(\d+\.?\s*(s|m|h|day)\s*)+$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.
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.
stringDirectory to keep pipeline Nextflow logs and reports.
string${params.outdir}/pipeline_infoBoolean whether to validate parameters against the schema at runtime
booleantrueShow all params when using --help
boolean