nf-core/phaseimpute
A bioinformatics pipeline to phase and impute genetic data
Define where the pipeline should find input data and save output data.
Path to comma or tab-separated file, yaml or json file containing information about the samples in the experiment.
string^\S+\.(csv|tsv|yaml|json)$Path to comma or tab-separated file, yaml or json file containing region of the genome to use (optional: if no file given, the whole genome will be used).
string^\S+\.(csv|tsv|yaml|json)$The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringShould the panel VCF files be renamed to match the reference genome (e.g. ‘chr1’ -> ‘1’)
booleanMaximum number of contigs name to print before resuming (i.e. show only subset and add ‘…’ at the end).
integer4Comma-separated list of samples to remove from the reference panel. Useful for benchmarking purposes.
string^([a-zA-Z0-9]+)(,[a-zA-Z0-9]+)*$Email address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringStep(s) to run.
stringImputation tool to use.
stringPublish each process output
booleantrue|falseArguments for the simulation mode
Depth of coverage for the simulated data
number1Genotype position to use to simulate the data
string^\S+\.(csv|tsv|yaml|json)$Arguments for the preparation of the reference panel
Path to comma or tab-separated file, yaml or json file containing reference panel information.
string^\S+\.(csv|tsv|yaml|json)$Should the reference panel be phased
booleantrue|falseShould the reference panel be normalized
booleantrue|falseShould the allele frequency for each variant (AC/AN fields necessary for Glimpse1 and the validation step) be computed using BCFtools fill-tags. This can be necessary if the fields are absent from the panel or if samples have been removed.
booleanModel type to use for GLIMPSE2_CHUNK
stringArguments for the imputation steps
Maximal number of individuals per batch for imputation.
integer100Path to comma or tab-separated file, yaml or json file containing genomic chunks to be used for imputation.
string^\S+\.(csv|tsv|yaml|json)$Path to comma or tab-separated file, yaml or json file containing reference panel information converted files for imputation.
string^\S+\.(csv|tsv|yaml|json)$Seed for random number generation in Stitch, QUILT and QUILT2 software
integer1Arguments for the concordance analysis of the imputed data
Path to comma or tab-separated file, yaml or json file containing samples truth files informations.
string^\S+\.(csv|tsv|yaml|json)$User-defined allele count bins used for rsquared computations.
string0 0.01 0.05 0.1 0.2 0.5^(\d+(\.\d+)? )+(\d+(\.\d+)?)$Minimum genotype likelihood probability P(G|R) in validation data. Set to zero to have no filter, if using gt-validation
number0.9^\d+(\.\d+)?$Minimum coverage in validation data. If FORMAT/DP is missing and -min_val_dp > 0, the program exits with an error. Set to zero to have no filter of if using –gt-validation
integer5^\d+$Reference genome related files and options required for the workflow.
Name of iGenomes reference.
stringPath to FASTA genome file.
string^\S+\.fn?a(sta)?(\.b?gz)?$Path to FASTA index genome file in .fai format.
string^\S+\.fn?a(sta)?(\.b?gz)?\.fai$Path to FASTA index genome file in .gzi format.
string^\S+\.fn?a(sta)?(\.b?gz)?\.gzi$Path to gmap genome file.
stringDo not load the iGenomes reference config.
booleanThe base path to the igenomes reference files
strings3://ngi-igenomes/igenomes/Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringLess common options for the pipeline, typically set in a config file.
Display version and exit.
booleanMethod used to save pipeline results to output directory.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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.
booleanCustom 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.
stringOptional two-column sample renaming file. First column a set of patterns, second column a set of corresponding replacements. Passed via MultiQC’s --replace-names option.
stringOptional TSV file with headers, passed to the MultiQC –sample_names argument.
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/phaseimpute/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).
booleanArguments to customize QUILT run
Buffer of region to perform imputation over. So imputation is run form regionStart-buffer to regionEnd+buffer, and reported for regionStart to regionEnd, including the bases of regionStart and regionEnd.
integer10000Number of generations since founding of the population to use for imputation.
integer100Arguments to customize STITCH run
Number of ancestral haplotypes to use for imputation. Refer to the documentation for the --K argument of STITCH for more information.
integer2