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)$You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See usage docs.
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringTruth id, sample name to define truth vcf
stringThe analysis type used by the input files
stringVariant types to benchmark
stringThe benchmarking methods to use. For germline small variants (SNV and INDEL) use happy and/or rtgtools, for somatic small variants (SNV and INDEL) use sompy and/or rtgtools, for structural variants use wittyer, truvari and/or svanalyzer, for copy number variations use wittyer and/or truvari. Use intersect to intersect BED files. Should be a comma-separate list of one or more of the following options: truvari, svanalyzer, happy, sompy, rtgtools, wittyer, intersect
string^((truvari|svanalyzer|happy|sompy|rtgtools|wittyer|intersect)?,?)*(?<!,)$Path to regions BED or VCF files. Works similar to Bcftools -R.
string^\S+\.(bed|vcf)?(\.gz)?$Regions BED files
Path to targets BED. Works similar to Bcftools -T. It will be only used with happy, sompy or rtgtools.
string^\S+\.(bed|vcf)?(\.gz)?$Target BED files
Path to false positive BED. Only applicable to happy and sompy tool.
string^\S+\.(bed)?(\.gz)?$Falsepositive BED files
Path to ambiguous BED. Only applicable to sompy tool.
string^\S+\.(bed)?(\.gz)?$Falsepositive BED files
Path to the golden set VCF files.
string^\S+\.vcf(\.gz)?$Truth or golden set VCF file, to be used for comparisons
The preprocessing steps to perform on the input files. Should be a comma-separated list of one or more of the following options: split_multiallelic, normalizate, deduplicate, prepy, filter_contigs
string^((normalize|split_multiallelic|deduplicate|prepy|filter_contigs)?,?)*(?<!,)$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^((homogenize|svync)?,?)*(?<!,)$Minimum SV size of variants to benchmark, 0 to disable
integerMaximum SV size of variants to benchmark, -1 to disable
integer-1Minimum Alele Frequency of variants to benchmark, Use -1 to disable
number-1Minimum number of read supporting variants to benchmark, Use, -1 to disable
integer-1Use bcftools expressions https://samtools.github.io/bcftools/bcftools.html#expressions to exclude variants
stringUse bcftools expressions https://samtools.github.io/bcftools/bcftools.html#expressions to include variants
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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.
stringReference genome related files and options required for the workflow.
Name of iGenomes reference.
stringIf 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 FASTA genome file.
string^\S+\.fn?a(sta)?(\.gz)?$This parameter is mandatory if --genome is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with --save_reference to save BWA index for future runs.
Path to FAI genome file.
string^\S+\.fai$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.
The SDF file needed to run rtgtools vcfeval
string^\S+\.sdf$This will be automatically generated by the pipeline when missing
Path to stratification BED files provided in a directory. This directory has to be given together with stratification_tsv, list BED files in stratification_tsv. Only applicable to happy tool.
stringStratification BED files
List the stratification BED files in this file, to be used with stratification_bed
string^\S+\.tsv$Stratification TSV file. List the stratification BED files in this file and use together with stratification_bed. Only applicable to happy tool
Do not load the iGenomes reference config.
booleanDo 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.
The base path to the igenomes reference files
strings3://ngi-igenomes/igenomes/Run liftover workflow: test,truth
string^((test|truth)?,?)*(?<!,)$Makes the use of liftover subworkflow, hg37 truth sets will liftover to hg38 and visa versa. Has to be either combined with --chain and --rename_chr.
Path to the chain file required for liftover.
string^\S+\.(chain|bed)?(\.gz)?$This parameter is mandatory if --liftover is true
Path to the ranaming chromosomes for lifting over.
string^\S+\.txt$This parameter is mandatory if --liftover is true
The dictionary file is required ofr liftover process. It has to be .dict of genome file used in the workflow.
string^\S+\.dict$This will be automatically generated by the pipeline when missing
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/masterIf 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.
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/variantbenchmarkingWarning: The -profile test samplesheet file itself contains remote paths. Setting this parameter does not alter the contents of that file.
Less common options for the pipeline, typically set in a config file.
Display version and exit.
booleanMethod used to save pipeline results to output directory.
stringThe 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})$An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.
Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Do not use coloured log outputs.
booleanDo not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringIncoming hook URL for messaging service. Currently, MS Teams and Slack are supported.
Custom 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