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-separated file containing information about the samples in the experiment.
string^\S+\.csv$You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See usage docs.
Region of the genome to use (optional: if no file given, the whole genome will be used). The file should be a comma-separated file with 3 columns, and a header row.
string^\S+\.csv$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]+)*$Email address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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.
stringStep(s) to run.
stringImputation tool to use.
stringMultiple tools separated with commas. Used when starting from --steps impute or --steps all.
glimpse1, glimpse2, quilt, stitchArguments for the simulation mode
Depth of coverage for the simulated data
integer1Genotype position to use to simulate the data
string^\S+\.(csv|tsv|txt)$Arguments for the preparation of the reference panel
Path to the reference panel or csv file with the list of panels
string^\S+\.(csv|tsv|txt)$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 VCFFIXUP tool. This can be necessary if the fields are absent from the panel or if samples have been removed.
booleanWhether to generate a binary reference file to be used with GLIMPSE2
stringModel type to use for GLIMPSE2_CHUNK
stringArguments for the imputation steps
Maximal number of individuals per batch for imputation.
integer100Path to comma-separated file containing tab-separated files with the genomic chunks to be used for imputation.
string^\S+\.csv$Seed for random number generation in Stitch and Quilt software
integer1Arguments for the concordance analysis of the imputed data
Path to comma-separated file containing information about the samples truth files in the experiment.
string^\S+\.csv$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.
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+$Reference genome related files and options required for the workflow.
Name of iGenomes reference.
stringIf using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. --genome GRCh38.
See the nf-core website docs for more details.
Path to FASTA genome file.
string^\S+\.fn?a(sta)?(\.gz)?$This parameter is mandatory if --genome is not specified.
Path to FASTA index genome file.
string^\S+\.fn?a(sta)?(\.gz)?\.fai$This parameter is optional even if --genome is not specified.
Path to gmap genome file.
stringThis parameter is optional. This is used to refine the imputation process to match the recombination event rate in your specie.
Do not load the iGenomes reference config.
booleanDo not load igenomes.config when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in igenomes.config.
The base path to the igenomes reference files
strings3://ngi-igenomes/igenomes/Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterIf you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.
Institutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringLess common options for the pipeline, typically set in a config file.
Display version and exit.
booleanMethod used to save pipeline results to output directory.
stringThe Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.
Email address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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$Do not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringIncoming hook URL for messaging service. Currently, MS Teams and Slack are supported.
Custom config file to supply to MultiQC.
stringCustom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
stringCustom MultiQC yaml file containing HTML including a methods description.
stringOptional two-column sample renaming file. First column a set of patterns, second column a set of corresponding replacements. Passed via MultiQC's --replace-names option.
stringOptional TSV file with headers, passed to the MultiQC --sample_names argument.
stringBoolean whether to validate parameters against the schema at runtime
booleantrueBase URL or local path to location of pipeline test dataset files
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/Arguments to customize QUILT run
Buffer of region to perform imputation over. So imputation is run form regionStart-buffer to regionEnd+buffer, and reported for regionStart to regionEnd, including the bases of regionStart and regionEnd.
integer10000Number of generations since founding of the population to use for imputation.
integer100Arguments to customize STITCH run
Path to comma-separated file containing tab-separated files describing the variable positions to be used for imputation. Refer to the documentation for the --posfile argument of STITCH for more information.
string^\S+\.(csv|tsv|txt)$Number of ancestral haplotypes to use for imputation. Refer to the documentation for the --K argument of STITCH for more information.
integer2