parameters.md

birneylab/stitchimpute pipeline parameters

A pipeline for imputing genotypes using STITCH, evaluating imputation performance against a ground truth, optimising imputation parameters, and refining the SNP set used

Input/output options

Define where the pipeline should find input data and save output data.

Parameter	Description	Type	Default	Required	Hidden
input	Path to comma-separated file containing information about the samples in the experiment. Help 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.	string		True
mode	Which branch of the pipeline to run. Can be imputation, grid_search, or snp_set_refinement	string	imputation
outdir	The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.	string		True
skip_chr	Chromosomes to skip Help Chromosomes from the reference provided that should not be imputed. Multiple chromosomes can be separated by commas. Es. "1,2,3".	string
grid_search_params	CSV files containing the values of the K and nGen parameters to be used for the grid search workflow Help Must have column names K and nGen. Each line corresponds to a combination of parameters to be tested.	string
snp_filtering_criteria	CSV file containing the threshold for inclusion of SNPs in the iterative refinement process Help By default the info_score value of the SNP is used for filtering if a ground truth is not provided, and the Pearson r^2 if a ground truth is provided. This can be changed with the filter_var parameter.	string
email	Email address for completion summary. Help 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.	string

Stitch options

Parameter	Description	Type	Default	Required	Hidden
stitch_posfile	Positions to run the imputation over Help Where to find file with positions to run. File is tab seperated with no header, one row per SNP, with col 1 = chromosome, col 2 = physical position (sorted from smallest to largest), col 3 = reference base, col 4 = alternate base. Bases are capitalized. Example first row: 1 1000 A G	string		True
stitch_K	Number of ancestral haplotypes Help See STITCH documentation for more details. Required for imputation mode.	integer
stitch_nGen	Number of generations since founding of the population Help See STITCH documentation for more details. Required for imputation mode.	integer

Reference genome options

Reference genome related files and options required for the workflow.

Parameter	Description	Type	Default	Required	Hidden
genome	Name of iGenomes reference. Help 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.	string
fasta	Path to FASTA genome file. Help 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.	string
igenomes_base	Directory / URL base for iGenomes references.	string	s3://ngi-igenomes/igenomes		True
igenomes_ignore	Do not load the iGenomes reference config. Help 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.	boolean			True

Ground truth

Parameter	Description	Type	Default	Required	Hidden
ground_truth_vcf	VCF file with ground truth calls Help Accepted format are vcf, vcf.gz, and bcf. Sample names must be identical to the sample names in the SM tag of the cram indicated in the samplesheet. Used to calculate correlation with the imputation results. Must contain FORMAT/DP and FORMAT/PL tags for all the variants.	string
freq_vcf	VCF file used to calculate allele frequencies. If not specified the realised frequencies in the imputation set are used. Help Accepted format are vcf, vcf.gz, and bcf. It is used by GLIMPSE concordance for determining MAF bins. Must contain an INFO/AF field or the field declared with --af-tag in GLIMPSE2_CONCORDANCE	string
downsample_coverage	To what average depth should the ground truth cram files be downsampled to? Help To what average depth should the ground truth cram files be downsampled to? If not specidied no downsampling is done. Must be a numeric value.	number
random_seed	Random seed used for downsampling	integer
filter_var	Perfromance metric used in filtering	string
glimpse2_concordance_bins	MAF bins for calculating validation performance Help Allele frequency bins used for r^2 computations. By default they should as MAF bins [0-0.5], while they should take the full range [0-1] if –use-ref-alt is used.	string	0 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40 0.45 0.5		True
glimpse2_concordance_allele_counts	Use default allele count bins Help Default allele count bins used for rsquared computations. AN field must be defined in the frequency file.	string			True
glimpse2_concordance_ac_bins	User-defined allele count bins Help User-defined allele count bins used for rsquared computations.	string			True
glimpse2_min_val_gl	Minimum genotype likelihood probability P(G	R) in validation data [set to zero to have no filter of if using –gt-validation]	integer	0
glimpse2_min_val_dp	Minimum coverage in validation data. If FORMAT/DP is missing and –minDP > 0, the program exits with an error. [set to zero to have no filter of if using –gt-validation]	integer	0		True
glimpse2_groups	Alternative to frequency bins: group bins are user defined, provided in a file.	string			True
glimpse2_samples	List of samples to process, one sample ID per line.	string			True

Institutional config options

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

Parameter	Description	Type	Default	Required	Hidden
custom_config_version	Git commit id for Institutional configs.	string	master		True
custom_config_base	Base directory for Institutional configs. Help 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.	string	https://raw.githubusercontent.com/nf-core/configs/master		True
config_profile_name	Institutional config name.	string			True
config_profile_description	Institutional config description.	string			True
config_profile_contact	Institutional config contact information.	string			True
config_profile_url	Institutional config URL link.	string			True

Max job request options

Set the top limit for requested resources for any single job.

Parameter	Description	Type	Default	Required	Hidden
max_cpus	Maximum number of CPUs that can be requested for any single job. Help Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1	integer	16		True
max_memory	Maximum amount of memory that can be requested for any single job. Help 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'	string	128.GB		True
max_time	Maximum amount of time that can be requested for any single job. Help 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'	string	240.h		True

Generic options

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

Parameter	Description	Type	Default	Required	Hidden
help	Display help text.	boolean			True
version	Display version and exit.	boolean			True
publish_dir_mode	Method used to save pipeline results to output directory. Help 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.	string	copy		True
email_on_fail	Email address for completion summary, only when pipeline fails. Help An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.	string			True
plaintext_email	Send plain-text email instead of HTML.	boolean			True
monochrome_logs	Do not use coloured log outputs.	boolean			True
hook_url	Incoming hook URL for messaging service Help Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.	string			True
validate_params	Boolean whether to validate parameters against the schema at runtime	boolean	True		True
validationShowHiddenParams	Show all params when using --help Help By 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.	boolean			True
validationFailUnrecognisedParams	Validation of parameters fails when an unrecognised parameter is found. Help By default, when an unrecognised parameter is found, it returns a warinig.	boolean			True
validationLenientMode	Validation of parameters in lenient more. Help Allows string values that are parseable as numbers or booleans. For further information see JSONSchema docs.	boolean			True