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 the samplesheet file containing information about the samples in the experiment.
string
^\S+\.(csv|tsv|json|yaml|yml)$
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
string
Email 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.
string
Reference genome related files and options required for the workflow.
The amount to pad each end of the target intervals to create bait intervals.
integer
100
^\S+\.bed(\.gz)?$
Directory for pre-built bwa index.
string
Directory for pre-built bwamem2 index.
string
Directory for pre-built bwameme’s learned index.
string
Path to the directory containing cadd annotations.
string
Path 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.
string
Name of iGenomes reference.
string
Path to a list of common SNP locations for Gens.
string
Path to interval list for Gens.
string
Path to female panel of normals for Gens.
string
Path to male panel of normals for Gens.
string
Path 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
string
s3://ngi-igenomes/igenomes/
Do not load the iGenomes reference config.
boolean
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)?$
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.
string
Name of the mitochondrial contig in the reference fasta file
string
chrM
File with mobile element references
string
^\S+\.tsv$
File with mobile element allele frequency references
string
^\S+\.csv$
Base path / URL for data used in the modules
string
Path to sentieon machine learning model file.
string
Path 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
string
Interval list file containing the intervals over which read counts are tabulated for CNV calling
string
File with gene ids that have reduced penetrance. For use with genmod
string
Vcf used for evaluating variant calls.
string
^\S+\.(csv|tsv|json|yaml|yml)$
If generated by the pipeline save the required indices/references in the results directory.
boolean
MT rank model config file for genmod.
string
SNV rank model config file for genmod.
string
SV rank model config file for genmod.
string
Directory for pre-built sdf index. Used by rtg/vcfeval
string
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|tsv|json|yaml|yml)$
Databases used for structural variant annotation in vcf format.
string
^\S+\.(csv|tsv|json|yaml|yml)$
Path to directory for target bed file.
string
^\S+\.bed(\.gz)?$
Path to variant catalog file
string
Path to a file containing internal ids and customer ids in csv format.
string
^\S+\.csv$
Path to a BED file containing markers used by verifybamid2.
string
Path to mean matrix file of genotype matrix. Used by verifybamid2.
string
Path to UD matrix file from SVD result of genotype matrix. Used by verifybamid2.
string
Path to vcf2cytosure blacklist file
string
^\S+\.bed$
Path to a VCF file containing annotations.
string
Path to a file containing the absolute paths to resources defined within the vcfanno toml file. One line per resource.
string
Path to the vcfanno toml file.
string
^\S+\.toml$
Path to the vcfanno lua file.
string
^\S+\.lua$
Path to vep’s cache directory.
string
Databases 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.
string
Path to a bed-like file exported by scout, which contains HGNC_IDs to be used in filter_vep.
string
Options 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.
string
Specifies whether or not to use bwa as a fallback aligner in case bwamem2 throws an error.
boolean
Specifies whether to generate a concatenated VCF file containing both nuclear & mitochondrial snv calls
boolean
After aligning the reads to a reference, extract alignments from specific regions/contigs and restrict the analysis to those regions/contigs.
boolean
false
Specifies the platform on which the reads were sequenced.
string
illumina
Method selection for ngs-bits samplegender
string
Can be specified as RNAME[:STARTPOS]. Multiple regions should be seperated by space
string
Specifies whether to run mitochondrial analysis for wes samples
boolean
Specifies whether to run rtgtools’ vcfeval
boolean
Specifies whether to generate and publish alignment files as cram instead of bam
boolean
Number of intervals to split your genome into (used to parallelize annotations)
integer
20
Disable specified subworkflows.
string
Disable specified tools.
string
Options to adjust parameters and filtering criteria for read alignments.
Specifies the alignment algorithm to use - available options are ‘bwamem2’, ‘bwa’, ‘bwameme’ and ‘sentieon’.
string
Specifies the alignment algorithm to use - available options are ‘bwamem2’, ‘bwa’ and ‘sentieon’.
string
Number of threads allocated for sorting alignment files (used only by bwameme)
integer
4
Memory allocated for mbuffer in megabytes (used only by bwameme)
integer
3072
Discard trimmed reads shorter than the given value
integer
40
Expected coverage to subsample mt alignment to.
integer
150
Subsampling seed used to influence which subset of mitochondrial reads is kept.
integer
30
Specifies whether duplicates reads should be removed prior to variant calling.
boolean
Options to adjust parameters and filtering criteria for variant calling.
Interval in the reference that will be used in the software. Used only by sentieon.
string
Bin size for CNVnator
integer
1000
Option for selecting the PCR indel model used by Sentieon Dnascope.
string
Specifies the variant caller to use - available options are ‘deepvariant’ and ‘sentieon’.
string
Specifies the variant types for sentieon variant caller.
string
Options 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.
string
File containing list of SO terms listed in the order of severity from most severe to lease severe for annotating genomic SVs.
string
Specify the version of the VEP cache provided to the --vep_cache
option.
integer
112
Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
string
master
Base directory for Institutional configs.
string
https://raw.githubusercontent.com/nf-core/configs/master
Institutional config name.
string
Institutional config description.
string
Institutional config contact information.
string
Institutional config URL link.
string
Less common options for the pipeline, typically set in a config file.
Display version and exit.
boolean
Method used to save pipeline results to output directory.
string
Email 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.
boolean
File size limit when attaching MultiQC reports to summary emails.
string
25.MB
^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
Do not use coloured log outputs.
boolean
Incoming hook URL for messaging service
string
Custom config file to supply to MultiQC.
string
Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
string
Custom MultiQC yaml file containing HTML including a methods description.
string
Boolean whether to validate parameters against the schema at runtime
boolean
true
Base URL or local path to location of pipeline test dataset files
string
https://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