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)$The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringTruth id, sample name to define truth vcf
stringThe analysis type used by the input files
stringVariant types to benchmark
stringThe benchmarking methods to use. For germline small variants (SNV and INDEL) use happy and/or rtgtools, for somatic small variants (SNV and INDEL) use sompy and/or rtgtools, for structural variants use wittyer, truvari and/or svanalyzer, for copy number variations use wittyer and/or truvari. Use intersect to intersect BED files. Should be a comma-separate list of one or more of the following options: truvari, svanalyzer, happy, sompy, rtgtools, wittyer, intersect
stringPath to regions BED or VCF files. Works similar to Bcftools -R.
string^\S+\.(bed|vcf)?(\.gz)?$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
stringThe standardization methods to perform on the input files. Should be a comma-separated list of one or more of the following options: homogenize, svync
stringMinimum SV size of variants to benchmark, 0 to disable
integerMaximum SV size of variants to benchmark, -1 to disable
integer-1Minimum Alele Frequency of variants to benchmark, Use -1 to disable
number-1Minimum number of read supporting variants to benchmark, Use, -1 to disable
integer-1Use bcftools expressions https://samtools.github.io/bcftools/bcftools.html#expressions to exclude variants
stringUse bcftools expressions https://samtools.github.io/bcftools/bcftools.html#expressions to include variants
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringReference genome related files and options required for the workflow.
Name of iGenomes reference.
stringPath to FASTA genome file.
string^\S+\.fn?a(sta)?(\.gz)?$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.
stringList the stratification BED files in this file, to be used with stratification_bed
string^\S+\.tsv$Do not load the iGenomes reference config.
booleanThe base path to the igenomes reference files
strings3://ngi-igenomes/igenomes/Run liftover workflow: test,truth
stringPath to the chain file required for liftover.
string^\S+\.(chain|bed)?(\.gz)?$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.
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.
stringBase path / URL for data used in the test profiles
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/variantbenchmarkingLess common options for the pipeline, typically set in a config file.
Display 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.
booleanDo 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.
stringBoolean whether to validate parameters against the schema at runtime
booleantrueBase URL or local path to location of pipeline test dataset files
stringhttps://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