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.

type: string
pattern: ^\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.

type: string
pattern: ^\S+\.csv$

The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.

required
type: string

Should the panel vcf files be renamed to match the reference genome (e.g. 'chr1' -> '1')

type: boolean
pattern: true|false

Comma-separated list of samples to remove from the reference panel. Useful for benchmarking purposes.

type: string

Email address for completion summary.

type: string
pattern: ^([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.

type: string

Step(s) to run.

type: string

Imputation tool to use.

type: string

Multiple tools separated with commas. Used when starting from --steps impute or --steps all.

This parameter must be a combination of the following values: glimpse1, glimpse2, quilt, stitch

Arguments for the simulation mode

Depth of coverage for the simulated data

type: integer
default: 1

Genotype position to use to simulate the data

type: string
pattern: ^\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

type: string
pattern: ^\S+\.(csv|tsv|txt)$

Should the reference panel be phased

type: boolean
pattern: true|false

Should the reference panel be normalized

type: boolean
pattern: true|false

Should 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.

type: boolean
pattern: true|false

Whether to generate a binary reference file to be used with GLIMPSE2

type: string

Arguments for the imputation steps

Path to comma-separated file containing tab-separated files with the genomic chunks to be used for imputation.

type: string
pattern: ^\S+\.csv$

Arguments for the concordance analysis of the imputed data

Path to comma-separated file containing information about the samples truth files in the experiment.

type: string
pattern: ^\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.

type: string
default: 0 0.01 0.05 0.1 0.2 0.5
pattern: ^(\d+(\.\d+)? )+(\d+(\.\d+)?)$

Minimum genotype likelihood probability P(G|R) in validation data. Set to zero to have no filter of if using gt-validation

type: number
default: 0.9
pattern: ^\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

type: integer
default: 5
pattern: ^\d+$

Reference genome related files and options required for the workflow.

Name of iGenomes reference.

type: string

If 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.

type: string
pattern: ^\S+\.fn?a(sta)?(\.gz)?$

This parameter is mandatory if --genome is not specified.

Path to FASTA index genome file.

type: string
pattern: ^\S+\.fn?a(sta)?(\.gz)?\.fai$

This parameter is optional even if --genome is not specified.

Path to gmap genome file.

type: string

This 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.

hidden
type: boolean

Do 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

hidden
type: string
default: s3://ngi-igenomes/igenomes/

Parameters used to describe centralised config profiles. These should not be edited.

Git commit id for Institutional configs.

hidden
type: string
default: master

Base directory for Institutional configs.

hidden
type: string
default: https://raw.githubusercontent.com/nf-core/configs/master

If 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.

hidden
type: string

Institutional config description.

hidden
type: string

Institutional config contact information.

hidden
type: string

Institutional config URL link.

hidden
type: string

Less common options for the pipeline, typically set in a config file.

Display version and exit.

hidden
type: boolean

Method used to save pipeline results to output directory.

hidden
type: string

The 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.

hidden
type: string
pattern: ^([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.

hidden
type: boolean

File size limit when attaching MultiQC reports to summary emails.

hidden
type: string
default: 25.MB
pattern: ^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$

Do not use coloured log outputs.

hidden
type: boolean

Incoming hook URL for messaging service

hidden
type: string

Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.

Custom config file to supply to MultiQC.

hidden
type: string

Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file

hidden
type: string

Custom MultiQC yaml file containing HTML including a methods description.

type: string

Optional 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.

type: string

Optional TSV file with headers, passed to the MultiQC --sample_names argument.

type: string

Boolean whether to validate parameters against the schema at runtime

hidden
type: boolean
default: true

Base URL or local path to location of pipeline test dataset files

hidden
type: string
default: https://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.

type: integer
default: 10000

Number of generations since founding of the population to use for imputation.

type: integer
default: 100

Arguments to customize STITCH run

type: integer
default: 1

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.

type: string
pattern: ^\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.

type: integer
default: 2