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#
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 |
||
|
Path to comma-separated file containing information about the samples in the experiment. |
|
type |
string |
|
pattern |
^\S+\.(csv|json)$ |
|
format |
file-path |
|
|
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 address for completion summary. |
|
type |
string |
|
pattern |
^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$ |
|
|
What format is the samplesheet in? (csv/json) |
|
type |
string |
|
enum |
csv, json |
|
default |
csv |
|
|
Path to a scoring file in PGS Catalog format. Multiple scorefiles can be specified using wildcards (e.g., |
|
type |
string |
|
|
A comma separated list of PGS score IDs, e.g. PGS000802 |
|
type |
string |
|
pattern |
PGS[0-9]{6} |
|
|
A comma separated list of PGS Catalog publications, e.g. PGP000001 |
|
type |
string |
|
pattern |
PGP[0-9]{6} |
|
|
A comma separated list of PGS Catalog EFO traits, e.g. EFO_0004214 |
|
type |
string |
|
|
DEPRECATED: A comma separated list of PGS Catalog EFO traits, e.g. EFO_0004214 |
|
type |
string |
|
|
Return only PGS tagged with exact EFO term (e.g. no PGS for child/descendant terms in the ontology) |
|
type |
boolean |
|
|
Copy harmonised genomes (plink2 pgen/pvar/psam files) to outdir |
|
type |
boolean |
|
|
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 |
||
|
Genome build of target genomes |
|
type |
string |
|
enum |
GRCh37, GRCh38 |
|
|
Lift scoring files to match your target genomes. Requires build information in the header of the scoring files. |
|
type |
boolean |
|
|
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 |
||
|
Allow matches of scoring file variants to multiallelic variants in the target dataset |
|
type |
boolean |
|
|
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 |
|
|
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 |
||
|
The method for PCA prediction. oadp: most accurate. adp: accurate but slow. sp: fast but inaccurate. |
|
type |
string |
|
enum |
oadp, sp, adp |
|
default |
oadp |
|
|
Method used for population/ancestry assignment |
|
type |
string |
|
enum |
Mahalanobis, RandomForest |
|
default |
RandomForest |
|
|
Population labels in reference psam to use for assignment |
|
type |
string |
|
default |
SuperPop |
|
|
Number of PCs used for population assignment |
|
type |
integer |
|
default |
5 |
|
|
Method used for normalisation of genetic ancestry |
|
type |
string |
|
enum |
empirical, mean, mean+var, empirical mean mean+var |
|
default |
empirical mean mean+var |
|
|
Number of PCs used for population normalisation |
|
type |
integer |
|
default |
4 |
|
|
Load allelic frequencies from reference panel when scoring target genomes |
|
type |
boolean |
|
default |
True |
|
|
Minimum MAF threshold in TARGET samples for variants to be included in the PCA. |
|
type |
number |
|
maximum |
1 |
|
minimum |
0 |
|
default |
0 |
|
|
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 |
||
|
Path to reference database. Must be set if –ref_samplesheet is not set. |
|
type |
string |
|
format |
file-path |
|
|
Path to a samplesheet that describes the structure of reference data. Must be set if –ref isn’t set. |
|
type |
string |
|
format |
file-path |
|
|
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 |
|
|
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 |
|
|
Exclude VARIANTS with percentage of missing genotype calls greater than a threshold (in reference genomes) |
|
type |
number |
|
maximum |
1 |
|
minimum |
0 |
|
default |
0.1 |
|
|
Exclude SAMPLES with percentage of missing genotype calls greater than a threshold (in reference genomes) |
|
type |
number |
|
maximum |
1 |
|
minimum |
0 |
|
default |
0.1 |
|
|
Exclude variants with minor allele frequency (MAF) lower than a threshold (in reference genomes) |
|
type |
number |
|
maximum |
1 |
|
minimum |
0 |
|
default |
0.05 |
|
|
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 |
|
|
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 |
|
|
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 |
|
|
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 |
|
|
Version of the default reference database |
|
type |
string |
|
default |
v0.1 |
|
|
Used to validate files in the reference database when built |
|
type |
string |
Developer options#
Control subworkflow execution, useful for debugging
type |
object |
|
default |
||
properties |
||
|
type |
boolean |
|
type |
boolean |
|
type |
boolean |
|
type |
boolean |
|
type |
boolean |
|
type |
boolean |
|
type |
boolean |
default |
True |
Max job request options#
Set the top limit for requested resources for any single job.
type |
object |
|
properties |
||
|
Maximum number of CPUs that can be requested for any single job. |
|
type |
integer |
|
default |
16 |
|
|
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 |
|
|
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 |
||
|
Display help text. |
|
type |
boolean |
|
|
Display version and exit. |
|
type |
boolean |
|
|
Method used to save pipeline results to output directory. |
|
type |
string |
|
enum |
symlink, rellink, link, copy, copyNoFollow, move |
|
default |
copy |
|
|
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})$ |
|
|
Send plain-text email instead of HTML. |
|
type |
boolean |
|
|
Do not use coloured log outputs. |
|
type |
boolean |
|
|
Incoming hook URL for messaging service |
|
type |
string |