Reference: Workflow parameters

The documentation below is automatically generated from the input schema and contains additional technical detail. Parameters in bold are required and must be set by the user.

Setting parameters

Parameters can be set in two ways:

1. Storing parameters in a configuration file using the -params-file option. See How to set parameters in a file for more details.

2. In a terminal using two dashes, e.g.:

$ nextflow run pgscatalog/pgsc_calc \
    -profile test,docker \
    --liftover \
    --target_build GRCh38

Parameters with a single dash (e.g. -profile) configure nextflow directly.

Setting parameters with a configuration file is the recommended method of working with the pipeline, because it helps you to keep track of your analysis.

For examples about setting max job request options, see How do I run pgsc_calc on larger datasets and more powerful computers?.

Advanced parameters

Some parameters have been hidden below to improve the readability of this page. You can view the entire list by running:

$ nextflow run pgscatalog/pgsc_calc --help

Or by downloading the schema and opening it in a text editor

Schema

pgscatalog/pgsc_calc pipeline parameters

The Polygenic Score Catalog Calculator is a nextflow pipeline for polygenic score calculation

https://raw.githubusercontent.com/pgscatalog/pgsc_calc/master/nextflow_schema.json
type	object

Input/output options

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

type	object
properties
input	Path to comma-separated file containing information about the samples in the experiment.
	type	string
	pattern	^\S+\.(csv|json)$
	format	file-path
outdir	The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
	type	string
	default	results
	format	directory-path
email	Email address for completion summary.
	type	string
	pattern	^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$
format	What format is the samplesheet in? (csv/json)
	type	string
	enum	csv, json
	default	csv
scorefile	Path to a scoring file in PGS Catalog format. Multiple scorefiles can be specified using wildcards (e.g., --scorefile \"path/to/scores/*.txt\")
	type	string
pgs_id	A comma separated list of PGS score IDs, e.g. PGS000802
	type	string
	pattern	PGS[0-9]{6}
pgp_id	A comma separated list of PGS Catalog publications, e.g. PGP000001
	type	string
	pattern	PGP[0-9]{6}
efo_id	A comma separated list of PGS Catalog EFO traits, e.g. EFO_0004214
	type	string
trait_efo	DEPRECATED: A comma separated list of PGS Catalog EFO traits, e.g. EFO_0004214
	type	string
efo_direct	Return only PGS tagged with exact EFO term (e.g. no PGS for child/descendant terms in the ontology)
	type	boolean
copy_genomes	Copy harmonised genomes (plink2 pgen/pvar/psam files) to outdir
	type	boolean
genotypes_cache	Path to a directory that can store relabelled genotypes (and the reference panel intersections and PCA with –run_ancestry) to speed up new PGS calculations on previously harmonized samples
	type	string
	format	directory-path

Compatibility options

Define parameters that control how scoring files and target genomes are made compatible with each other

type	object
default
properties
target_build	Genome build of target genomes
	type	string
	enum	GRCh37, GRCh38
liftover	Lift scoring files to match your target genomes. Requires build information in the header of the scoring files.
	type	boolean
min_lift	Minimum proportion of variants required to successfully remap a scoring file to a different genome build.
	type	number
	maximum	1
	minimum	0
	default	0.95

Matching options

Define how variants are matched across scoring files and target genomes.

type	object
default
properties
keep_multiallelic	Allow matches of scoring file variants to multiallelic variants in the target dataset
	type	boolean
keep_ambiguous	Keep matches of scoring file variants to strand ambiguous variants (e.g. A/T and C/G SNPs) in the target dataset. This assumes the scoring file and target dataset report variants on the same strand.
	type	boolean
min_overlap	Minimum proportion of variants present in both the score file and input target genomic data
	type	number
	maximum	1
	minimum	0
	default	0.75

Genetic ancestry options

Parameters used to control genetic ancestry similarity analysis on TARGET samples and variants included in PCA

type	object
default
properties
projection_method	The method for PCA prediction. oadp: most accurate. adp: accurate but slow. sp: fast but inaccurate.
	type	string
	enum	oadp, sp, adp
	default	oadp
ancestry_method	Method used for population/ancestry assignment
	type	string
	enum	Mahalanobis, RandomForest
	default	RandomForest
ref_label	Population labels in reference psam to use for assignment
	type	string
	default	SuperPop
n_popcomp	Number of PCs used for population assignment
	type	integer
	default	5
normalization_method	Method used for normalisation of genetic ancestry
	type	string
	enum	empirical, mean, mean+var, empirical mean mean+var
	default	empirical mean mean+var
n_normalization	Number of PCs used for population normalisation
	type	integer
	default	4
load_afreq	Load allelic frequencies from reference panel when scoring target genomes
	type	boolean
	default	True
pca_maf_target	Minimum MAF threshold in TARGET samples for variants to be included in the PCA.
	type	number
	maximum	1
	minimum	0
	default	0
pca_geno_miss_target	Maximum genotype missingness threshold in TARGET samples for variants to be included in the PCA.
	type	number
	maximum	1
	minimum	0
	default	0.1

Reference options

Define how genomes and variants in REFERENCE panel are defined and processed for PCA

type	object
default
properties
run_ancestry	Path to reference database. Must be set if –ref_samplesheet is not set.
	type	string
	format	file-path
ref_samplesheet	Path to a samplesheet that describes the structure of reference data. Must be set if –ref isn’t set.
	type	string
	format	file-path
hg19_chain	Path to a UCSC chain file for converting from hg19 to hg38. Needed if lifting over a custom scoring file.
	type	string
	pattern	.*chain.gz$
	format	file-path
hg38_chain	Path to a UCSC chain file for converting from hg38 to hg19. Needed if lifting over a custom scoring file.
	type	string
	pattern	.*chain.gz$
	format	file-path
geno_ref	Exclude VARIANTS with percentage of missing genotype calls greater than a threshold (in reference genomes)
	type	number
	maximum	1
	minimum	0
	default	0.1
mind_ref	Exclude SAMPLES with percentage of missing genotype calls greater than a threshold (in reference genomes)
	type	number
	maximum	1
	minimum	0
	default	0.1
maf_ref	Exclude variants with minor allele frequency (MAF) lower than a threshold (in reference genomes)
	type	number
	maximum	1
	minimum	0
	default	0.05
hwe_ref	Exclude variants with Hardy-Weinberg equilibrium exact test p-values below a threshold (in reference genomes)
	type	number
	maximum	1
	minimum	0
	default	0.0001
indep_pairwise_ref	Used to generate a list of variants in approximate linkage equilibrium in reference genomes. Window size - step size - unphased hardcall r^2 threshold.
	type	string
	default	1000 50 0.05
ld_grch37	Path to a file that contains areas of high linkage disequilibrium in the reference data (build GRCh37).
	type	string
	default	/Users/bwingfield/Documents/projects/pgsc_calc/assets/ancestry/high-LD-regions-hg19-GRCh37.txt
	format	file-path
ld_grch38	Path to a file that contains areas of high linkage disequilibrium in the reference data (build GRCh38).
	type	string
	default	/Users/bwingfield/Documents/projects/pgsc_calc/assets/ancestry/high-LD-regions-hg38-GRCh38.txt
	format	file-path
ref_format_version	Version of the default reference database
	type	string
	default	v0.1
ancestry_checksums	Used to validate files in the reference database when built
	type	string

Developer options

Control subworkflow execution, useful for debugging

type	object
default
properties
only_bootstrap	type	boolean
only_input	type	boolean
only_compatible	type	boolean
only_match	type	boolean
only_projection	type	boolean
only_score	type	boolean
skip_ancestry	type	boolean
	default	True

Max job request options

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

type	object
properties
max_cpus	Maximum number of CPUs that can be requested for any single job.
	type	integer
	default	16
max_memory	Maximum amount of memory that can be requested for any single job.
	type	string
	pattern	^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
	default	128.GB
max_time	Maximum amount of time that can be requested for any single job.
	type	string
	pattern	^(\d+\.?\s*(s|m|h|d|day)\s*)+$
	default	240.h

Generic options

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

type	object
properties
help	Display help text.
	type	boolean
version	Display version and exit.
	type	boolean
publish_dir_mode	Method used to save pipeline results to output directory.
	type	string
	enum	symlink, rellink, link, copy, copyNoFollow, move
	default	copy
email_on_fail	Email address for completion summary, only when pipeline fails.
	type	string
	pattern	^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$
plaintext_email	Send plain-text email instead of HTML.
	type	boolean
monochrome_logs	Do not use coloured log outputs.
	type	boolean
hook_url	Incoming hook URL for messaging service
	type	string