nf-core/variantbenchmarking
A nextflow variant benchmarking pipeline - premature
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)$You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See usage docs.
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringSample id
stringThe analysis type used by the input files
stringThe benchmarking methods to use. Should be a comma-separate list of one or more of the following options: truvari, svanalyzer, happy, sompy, rtgtools, wittyer
stringSMALL: Path to the high confidence BED or VCF files.
string^\S+\.(bed|vcf)?(\.gz)?$SMALL: High confidence BED files
SMALL: Path to the golden set VCF files.
string^\S+\.(vcf)?(\.gz)?$SMALL: Truth or golden set VCF file, to be used for comparisons
SNVs: Path to the high confidence BED or VCF files.
string^\S+\.(bed|vcf)?(\.gz)?$SNVs: High confidence BED files
SNVs: Path to the golden set VCF files.
string^\S+\.(vcf)?(\.gz)?$SNVs: Truth or golden set VCF file, to be used for comparisons
INDELs: Path to the high confidence BED or VCF files.
string^\S+\.(bed|vcf)?(\.gz)?$INDELs: High confidence BED files
INDELs: Path to the golden set VCF files.
string^\S+\.(vcf)?(\.gz)?$INDELs: Truth or golden set VCF file, to be used for comparisons
SV: Path to the high confidence BED or VCF files.
string^\S+\.(bed|vcf)?(\.gz)?$SV: High confidence BED files
SV: Path to the golden set VCF files.
string^\S+\.(vcf)?(\.gz)?$SV: Truth or golden set VCF file, to be used for comparisons
CNV: Path to the high confidence BED or VCF files.
string^\S+\.(bed|vcf)?(\.gz)?$CNV: High confidence BED files
CNV: Path to the golden set VCF files.
string^\S+\.(vcf)?(\.gz)?$CNV: Truth or golden set VCF file, to be used for comparisons
The preprocessing steps to perform on the input files. Should be a comma-separated list of one or more of the following options: normalization, deduplication, prepy, filter_contigs
stringThe standardization methods to perform on the input files. Should be a comma-separated list of one or more of the following options: homogenize, svync
stringMinimum SV size of variants to benchmark, 0 to disable , Default:30
integerMaximum SV size of variants to benchmark, -1 to disable , Default:-1
integerMinimum Alele Frequency of variants to benchmark, Use -1 to disable , Default:-1
numberMinimum number of read supporting variants to benchmark, Use, -1 to disable , Default:-1
integerUse bcftools expressions https://samtools.github.io/bcftools/bcftools.html#expressions to exclude variants. Default:null
stringUse bcftools expressions https://samtools.github.io/bcftools/bcftools.html#expressions to include variants. Default:null
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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)?$This parameter is mandatory if --genome is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with --save_reference to save BWA index for future runs.
Path to FAI genome file.
stringThis parameter is mandatory if --genome is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with --save_reference to save BWA index for future runs.
The SDF file needed to run rtgtools vcfeval
string^\S+\.sdf$This will be automatically generated by the pipeline when missing
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.
Do not load the truth reference config.
booleanDo not load truth.config when running the pipeline. In this case user need to provide necessary truth files. You may choose this option if you observe clashes between custom parameters and those supplied in truth.config.
Run liftover workflow
booleanMakes the use of liftover subworkflow, hg37 truth sets will liftover to hg38 and visa versa. Has to be either combined with itruth.config or --chain and --rename_chr.
Path to the chain file sey required for liftover.
string^\S+\.(chain|bed)?(\.gz)?$This parameter is mandatory if --liftover is true and --genome is not specified and --itruth is false. A chain can be found under itruth files and can be used together with --genome.
Path to the ranaming chromosomes for lifting over.
string^\S+\.txt$This parameter is mandatory if --liftover is true and --genome is not specified and --itruth is false. A rename can be found under assets/rename_contigs or can be used together with --genome.
The dictionary file is required ofr liftover process. It has to be .dict of genome file used in the workflow.
string^\S+\.dict$This will be automatically generated by the pipeline when missing
Parameters used to describe centralized config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterIf you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.
Institutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1
Maximum amount of memory that can be requested for any single job.
string128.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$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.
string240.h^(\d+\.?\s*(s|m|h|d|day)\s*)+$Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. --max_time '2.h'
Less common options for the pipeline, typically set in a config file.
Display help text.
booleanDisplay version and exit.
booleanMethod used to save pipeline results to output directory.
stringThe Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.
Email address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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
booleantrueShow all params when using --help
booleanBy 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.
booleanBy default, when an unrecognised parameter is found, it returns a warinig.
Validation of parameters in lenient more.
booleanAllows 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
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/