nf-core/variantbenchmarking
Pipeline to evaluate and validate the accuracy of variant calling methods in genomic research
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|tsv|yaml|yml|json)$
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
string
Truth id, sample name to define truth vcf
string
The analysis type used by the input files
string
Variant types to benchmark
string
The benchmarking methods to use. For germline small variants (SNV and INDEL) use happy and/or rtgtools, for somatic small variants (SNV and INDEL) use sompy and/or rtgtools, for structural variants use wittyer, truvari and/or svanalyzer, for copy number variations use wittyer and/or truvari. Use intersect to intersect BED files. Should be a comma-separate list of one or more of the following options: truvari, svanalyzer, happy, sompy, rtgtools, wittyer, intersect
string
Path to regions BED or VCF files. Works similar to Bcftools -R.
string
^\S+\.(bed|vcf)?(\.gz)?$
Path to targets BED. Works similar to Bcftools -T. It will be only used with happy, sompy or rtgtools.
string
^\S+\.(bed|vcf)?(\.gz)?$
Path to false positive BED. Only applicable to happy and sompy tool.
string
^\S+\.(bed)?(\.gz)?$
Path to ambiguous BED. Only applicable to sompy tool.
string
^\S+\.(bed)?(\.gz)?$
Path to the golden set VCF files.
string
^\S+\.vcf(\.gz)?$
The preprocessing steps to perform on the input files. Should be a comma-separated list of one or more of the following options: split_multiallelic, normalizate, deduplicate, prepy, filter_contigs
string
The standardization methods to perform on the input files. Should be a comma-separated list of one or more of the following options: homogenize, svync
string
Minimum SV size of variants to benchmark, 0 to disable
integer
Maximum SV size of variants to benchmark, -1 to disable
integer
-1
Minimum Alele Frequency of variants to benchmark, Use -1 to disable
number
-1
Minimum number of read supporting variants to benchmark, Use, -1 to disable
integer
-1
Use bcftools expressions https://samtools.github.io/bcftools/bcftools.html#expressions to exclude variants
string
Use bcftools expressions https://samtools.github.io/bcftools/bcftools.html#expressions to include variants
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.
Name of iGenomes reference.
string
Path to FASTA genome file.
string
^\S+\.fn?a(sta)?(\.gz)?$
Path to FAI genome file.
string
^\S+\.fai$
The SDF file needed to run rtgtools vcfeval
string
^\S+\.sdf$
Path to stratification BED files provided in a directory. This directory has to be given together with stratification_tsv, list BED files in stratification_tsv. Only applicable to happy tool.
string
List the stratification BED files in this file, to be used with stratification_bed
string
^\S+\.tsv$
Do not load the iGenomes reference config.
boolean
The base path to the igenomes reference files
string
s3://ngi-igenomes/igenomes/
Run liftover workflow: test,truth
string
Path to the chain file required for liftover.
string
^\S+\.(chain|bed)?(\.gz)?$
Path to the ranaming chromosomes for lifting over.
string
^\S+\.txt$
The dictionary file is required ofr liftover process. It has to be .dict of genome file used in the workflow.
string
^\S+\.dict$
Parameters used to describe centralized 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
Base path / URL for data used in the test profiles
string
https://raw.githubusercontent.com/nf-core/test-datasets/variantbenchmarking
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
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