nf-core/raredisease
Call and score variants from WGS/WES of rare disease patients.
1.1.1
). 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.
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.
number
100
^\S+\.bed(\.gz)?$
Directory for pre-built bwa index.
string
Directory for pre-built bwamem2 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
GRCh38
Path to a list of common SNP locations for Gens.
string
Path to interval list for Gens.
string
Path to 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$
Directory / URL base for iGenomes references.
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
Path to sentieon machine learning model file.
string
Path to mitochondrial FASTA genome file.
string
^\S+\.fn?a(sta)?(\.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
If generated by the pipeline save the required indices/references in the results directory.
boolean
SNV rank model config file for genmod.
string
SV rank model config file for genmod.
string
Path to the genome dictionary file
string
^\S+\.dict$
Databases used for structural variant annotation.
string
Path to directory for target bed file.
string
^\S+\.bed(\.gz)?$
Path to variant catalog file
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
Path to the file containing HGNC_IDs of interest on separate lines.
string
Options 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.
string
Specifies whether or not to run gens preprocessing subworkflow.
boolean
Specifies which analysis type for the pipeline- either ‘wgs’,‘wes’,‘mito’. This changes resources consumed and tools used.
string
Specifies whether to generate and publish alignment files as cram instead of bam
boolean
Specifies whether or not to skip CNV calling.
boolean
Specifies whether or not to skip the subworkflow that analyses mitochondrial genome separate from the nuclear genome.
boolean
Specifies whether or not to skip annotate SNV subworkflow.
boolean
Specifies whether or not to skip annotate structural variant subworkflow.
boolean
Options to adjust parameters and filtering criteria for read alignments.
Specifies the alignment algorithm to use - available options are ‘bwamem2’ and ‘sentieon’.
string
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
string
Indicates whether the sample library is amplified using PCR or not. Set to false for PCR Free samples.
boolean
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.
Specify the version of the VEP cache provided to the --vep_cache
option.
integer
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
Set the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer
16
Maximum amount of memory that can be requested for any single job.
string
128.GB
^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
Maximum amount of time that can be requested for any single job.
string
240.h
^(\d+\.?\s*(s|m|h|d|day)\s*)+$
Less common options for the pipeline, typically set in a config file.
Display help text.
boolean
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
Show all params when using --help
boolean
Validation of parameters fails when an unrecognised parameter is found.
boolean
Validation of parameters in lenient more.
boolean