Reference: Input Parameters/Flags

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

Parameter 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

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
	default	None
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
pgs_id	A comma separated list of PGS score IDs, e.g. PGS000802
	type	string
	default	None
pgp_id	A comma separated list of PGS Catalog publications, e.g. PGP000001
	type	string
	default	None
trait_efo	A comma separated list of PGS Catalog EFO traits, e.g. EFO_0004214
	type	string
	default	None
efo_direct	Return only PGS tagged with exact EFO term (e.g. no PGS for child/descendant terms in the ontology)
	type	boolean
target_build	Genome build of input data
	type	string
	enum	GRCh37, GRCh38
ref	Path to reference database
	type	string
	default	https://gitlab.ebi.ac.uk/nebfield/test-datasets/-/raw/master/pgsc_calc/reference_data/pgsc_calc_ref.sqlar
vzs	Assume plink inputs (.bim / .pvar) are compressed with zstd
	type	boolean
copy_genomes	Copy harmonised genomes (plink2 pgen/pvar/psam files) to outdir
	type	boolean
genotypes_cache	type	string
	default	None
outdir	Path to the output directory where the results will be saved.
	type	string
	default	./results
email	Email address for completion summary.
	type	string
	pattern	^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$

Variant Matching QC & Filtering

type	object
default
properties
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
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
tracedir	Directory to keep pipeline Nextflow logs and reports.
	type	string
	default	${params.outdir}/pipeline_info
validate_params	Boolean whether to validate parameters against the schema at runtime
	type	boolean
	default	True
show_hidden_params	Show all params when using –help
	type	boolean
enable_conda	Run this workflow with Conda. You can also use ‘-profile conda’ instead of providing this parameter.
	type	boolean
singularity_pull_docker_container	Instead of directly downloading Singularity images for use with Singularity, force the workflow to pull and convert Docker containers instead.
	type	boolean
platform	What platform is the pipeline executing on?
	type	string
	enum	amd64, arm64
	default	amd64
parallel	Enable parallel calculation of scores. This is I/O and RAM intensive.
	type	boolean