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#

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

default

True

  • hook_url

type

string

  • version

type

boolean

  • config_profile_name

type

string

  • config_profile_description

type

string

  • custom_config_version

type

string

default

master

  • custom_config_base

type

string

default

https://raw.githubusercontent.com/nf-core/configs/master

  • config_profile_contact

type

string

  • config_profile_url

type

string