nf-core/genomicrelatedness
Bioinformatics pipeline for estimating genetic relatedness from low-coverage whole-genome sequencing (sWGS) data
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$The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringReference genome related files and options required for the workflow.
Path to FASTA reference genome file.
string^\S+\.fn?a(sta)?(\.gz)?$Path to FASTA index (.fai) file for the reference genome.
string^\S+\.fn?a(sta)?(\.gz)?\.fai$Path to sequence dictionary (.dict) for the reference genome.
string^\S+\.dict$Path to directory containing the BWA-MEM2 index for the reference genome.
stringPath to directory containing the intervals in bed format.
stringNumber of interval files to split the reference genome into for parallel processing.
integerMaximum number of intervals per interval file for parallel processing.
integerOptions for providing an existing known variant set or generating one via bootstrapping.
Path to known variant set vcf file.
string,null^\S+\.vcf\.gz$Path to known variant set tabix index tbi file.
string,null^\S+\.vcf\.gz\.tbi$Number of bootstrapping rounds to perform when generating a variant set.
integer,nullList of scaffolds (e.g., chromosome or contig names) to include using vcftools. Can be passed as single string, array of strings, path to text file (including .bed). Leave empty to choose all by default.
string,array,nullList of scaffolds (e.g., chromosome or contig names) to exclude using vcftools. Can be passed as single string, array of strings, path to text file (including .bed). Leave empty to disable exclusion.
string,array,nullOptions for pipeline stages to run.
Whether to perform hard filtering of variants.
booleanWhether to skip Base Quality Score Recalibration (BQSR) on the aligned reads.
booleanWhether to skip the variant calling stage to identify variants from the aligned reads.
booleanWhether to skip the relatedness estimation stage.
booleanParameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringLess common options for the pipeline, typically set in a config file.
Display version and exit.
booleanMethod used to save pipeline results to output directory.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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.
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.
stringDisplay the help message.
boolean,stringDisplay the full detailed help message.
booleanDisplay hidden parameters in the help message (only works when —help or —help_full are provided).
boolean