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:

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

This pipeline applies scoring files from the PGS Catalog to target set(s) of genotyped samples

https://raw.githubusercontent.com/pgscatalog/pgsc_calc/master/nextflow_schema.json
type	object
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
skip_ancestry	default	True
hook_url	type	string
version	type	boolean
config_profile_name	type	string
config_profile_description	type	string
custom_config_version	type	string
custom_config_version	default	master
custom_config_base	type	string
custom_config_base	default	https://raw.githubusercontent.com/nf-core/configs/master
config_profile_contact	type	string
config_profile_url	type	string
validationFailUnrecognisedParams	type	boolean
validationLenientMode	type	boolean
validationShowHiddenParams	type	boolean

Input/output options#

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

type	object
properties
input	Path to input samplesheet
	type	string
	format	file-path
format	Format of input samplesheet
	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
	format	file-path
pgs_id	A comma separated list of PGS score IDs, e.g. PGS000802
	type	string
pgp_id	A comma separated list of PGS Catalog publications, e.g. PGP000001
	type	string
trait_efo	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
outdir	Path to the output directory where the results will be saved.
	type	string
	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})$

Ancestry options#

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

Reference options#

Define how reference genomes are defined and processed

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.
ref_samplesheet	type	string
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
	format	file-path
geno_ref	Exclude variants with missing call frequencies greater than a threshold (in reference genomes)
	type	number
	maximum	1
	minimum	0
	default	0.1
mind_ref	Exclude samples with missing call frequencies greater than a threshold (in reference genomes)
	type	number
	maximum	1
	minimum	0
	default	0.1
maf_ref	Exclude variants with allele frequency 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
	format	file-path
ld_grch38	Path to a file that contains areas of high linkage disequilibrium in the reference data (build GRCh38).
	type	string
	format	file-path
ref_format_version	type	string
ref_format_version	default	v0.1
ancestry_checksums	type	string

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
fast_match	Enable fast matching, which significantly increases RAM usage (32GB minimum recommended)
	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

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\|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
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
validate_params	Boolean whether to validate parameters against the schema at runtime
	type	boolean
	default	True

Contents

About the project

Useful links

Reference: Workflow parameters