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

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