parameters.md

birneylab/flexlmm pipeline parameters

Flexible linear mixed model framework for Genome Wide Association Studies

Genotype options

Different format options for the input genotypes.

Parameter	Description	Type	Default	Required	Hidden
vcf	Input genotypes in vcf format. Can be bgzip compressed.	string
bcf	Input genotypes in bcf format. Can be bgzip compressed.	string
bgen	Input genotypes in Oxford bgen format. Requires also gen and sample files to be specified..	string
sample	sample file for Oxford bgen input format	string
bed	Input genotypes in bed format. Requires also bim and fam files to be specified.	string
bim	bim file for bed input format	string
fam	fam file for bed input format	string
ped	Input genotypes in ped format. Requires also map_f files to be specified.	string
map_f	map file for ped input format	string
pgen	Input genotypes in pgen format. Requires also pvar and psam files to be specified.	string
psam	psam file for pgen input format	string
pvar	pvar file for pgen input format	string

Input/output options

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

Parameter	Description	Type	Default	Required	Hidden
outdir	The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.	string		True
pheno	Phenotype file in PLINK2 format Help The first columns must be either FID/IID or just IID (in which case the FID is assumed to be 0). A primary header line is required and it should begin with 'FID', '#FID', 'IID', or '#IID'). Differently from the plink2 format, additional header lines (beginning with '#', not immediately followed by 'FID'/'IID') are NOT permitted before the primary header line. IID must match sample names in vcf. FID is tolerated but not used. Missing values should be specified as NA and not following plink2 conventions (i.e. -9 is NOT seen as missing). See an example file	string		True
covar	Categorical covariates. Same format as pheno. Help Columns cannot be named 'x', 'y', 'ID', '#ID', 'FID', or '#FID', or have the same name of columns in qcovar . See an example file	string
qcovar	Quantitative covariates. Same format as pheno. Help Columns cannot be named 'x', 'y', 'ID', '#ID', 'FID', or '#FID', or have the same name of columns in covar . See an example file	string
freq	plink2-type frequency file for GRM calculations Help Can be obtained with plink2 with the command --freq. Variants included should all be biallelic and have IDs matching the ones in the main genome file provided.	string
maf_min	Exclude from the analysis genetic variants with a Minor Allele Frequency (MAF) under this value	number
use_dosage	Should genotype dosages be used or hard calls? Help If set to true, the genotype dosages are converted to hard calls without missingness. If you want to use more advanced conversion criteria use the ext.args* slot of the VCF_TO_PGEN and FIT_MODEL processes.	boolean	True
select_chr	Restrict analysis to a set of chromosomes Help Comma-separated string of chromosome names in vcf. If not specified all chromosomes are used. If a chromosome is specified still the rest of the genome is used to evaluate the LOCO relatedness matrix. Example: '1,2,3'	string
select_pheno	Restrict analysis to a set of phenotypes Help Comma-separated string of column names in pheno to be used as phenotypes. If not specified all the columns of pheno are used. Example: 'pheno1,pheno2'	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

Statistical parameters

Parameter	Description	Type	Default	Required	Hidden
quantile_normalise	Should the phenotypes be quantile normalised? Help Forces phenotypes to a N(0, 1) distribution.	boolean
standardise	Should the phenotypes be mean-centered and variance-scaled?	boolean
null_model_formula	R-style formula for the outer model that you want to use as a baseline. Help A string like 'y ~ cov1'. Here 'y' can be used to refer to the phenotype, and 'x' can be used to refer to the genotype. Column names in covar and qcovar can also be used. See https://www.rdocumentation.org/packages/stats/versions/3.6.2/topics/formula for more information on R formulas.	string		True
model_formula	R-style formula for the nested model that includes the variable of interest Help Similar to null_model_formula. Must contain all the terms in null_model_formula plus at least an extra one. You can also include GxE terms (es. 'y ~ x + x:cov1 + cov1'), and dominance terms ('y ~ x + I(x == 1) + cov1'). Arithmetic operations such as 'I(x == 1)' must be encapsulated in I() for proper evaluation.	string		True
permutations	Number of permutations to be performed	integer	10
p_thr	Nominal significance threshold	number	0.05

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

Other parameters

Parameter	Description	Type	Default	Required	Hidden
maf_min_grm		number	0.1