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.
string
Email 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.
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
If none provided, will be generated automatically from the FASTA reference.
Directory for pre-built bwamem2 index.
string
If none provided, will be generated automatically from the FASTA reference.
Directory for pre-built bwameme's learned index.
string
If none provided, will be generated automatically from the FASTA reference.
Path to the directory containing cadd annotations.
string
This 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.
string
This model is required for generating a cnv calls when using GermlineCNVCaller.
Name of iGenomes reference.
string
If 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.
string
Locations of gnomad SNPs with a high enough BAF.
Path to interval list for Gens.
string
This file contains the binning intervals used for CollectReadCounts.
Path to female panel of normals for Gens.
string
The female panel used to run DenoiseReadCounts.
Path to male panel of normals for Gens.
string
The 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.
boolean
Do 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.
string
This folder is a flat structure with file names that map to the config.
Name of the mitochondrial contig in the reference fasta file
string
chrM
Used 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.
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
Produced 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
string
Generated by GATK4 preprocessintervals. It needs to be the same as the intervals used to generate the ploidy and cnv models.
File with gene ids that have reduced penetrance. For use with genmod
string
Vcf 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.
boolean
The saved references can be used for future pipeline runs, reducing processing times.
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
If 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
string
Should 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 VCF file containing annotations.
string
Can be used to supply case-specific annotations in addition to those provided using --vcfanno_resources
Path to a file containing the absolute paths to resources defined within the vcfanno toml file. One line per resource.
string
If 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.
string
If 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.
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
errorStrategy needs to be set to ignore for the bwamem2 process for the fallback to work. Turned off by default.
Specifies the platform on which the reads were sequenced.
string
illumina
Method selection for ngs-bits samplegender
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
Specifies whether or not to skip trimming with fastp.
boolean
Specifies whether or not to skip gens preprocessing subworkflow.
boolean
Specifies whether or not to skip CNV calling using GATK's GermlineCNVCaller
boolean
Specifies whether or not to skip peddy.
boolean
Specifies whether or not to skip calling mobile elements, and the subsequent annotation step.
boolean
Specifies whether or not to skip annotation of mobile elements.
boolean
Specifies whether or not to skip annotation of mitochondrial variants.
boolean
Specifies whether or not to subsample mt alignment.
boolean
Specifies whether or not to skip annotation of repeat expansions.
boolean
Specifies whether or not to skip calling of repeat expansions.
boolean
Specifies whether or not to skip smncopynumbercaller.
boolean
Specifies whether or not to skip annotate SNV subworkflow.
boolean
Specifies whether or not to skip nuclear and mitochondrial SNV calling and annotation.
boolean
Specifies whether or not to skip annotate structural variant subworkflow.
boolean
Specifies whether or not to skip nuclear and mitochondrial SV calling and annotation.
boolean
Specifies whether or not to skip the vcf2cytosure subworkflow
boolean
true
vcf2cytosure 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'.
boolean
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
To know more about this parameter check bwameme documentation.
Memory allocated for mbuffer in megabytes (used only by bwameme)
integer
3072
To know more about this parameter check bwameme documentation.
Discard trimmed reads shorter than the given value
integer
40
Minimum length of reads after adapter trimming. Shorter reads are discarded.
Expected coverage to subsample mt alignment to.
integer
150
To know more about this parameter check samtools' view documentation.
Subsampling seed used to influence which subset of mitochondrial reads is kept.
integer
30
To know more about this parameter check samtools' view documentation.
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
Bin size for CNVnator
integer
1000
Option for selecting the PCR indel model used by Sentieon Dnascope.
string
PCR 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'.
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
For 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.
string
For 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.
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
If 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.
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
Use 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.
string
128.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.
string
240.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.
boolean
Display version and exit.
boolean
Method used to save pipeline results to output directory.
string
The 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.
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
Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.
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
By 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.
boolean
By default, when an unrecognised parameter is found, it returns a warinig.
Validation of parameters in lenient more.
boolean
Allows string values that are parseable as numbers or booleans. For further information see JSONSchema docs.
Base URL or local path to location of pipeline test dataset files
string
https://raw.githubusercontent.com/nf-core/test-datasets/