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 |
||
|
type |
string |
default |
/Users/bwingfield/Documents/projects/pgsc_calc/assets/ancestry/checksums.txt |
Input/output options#
Define where the pipeline should find input data and save output data.
type |
object |
|
properties |
||
|
Path to input samplesheet |
|
type |
string |
|
format |
file-path |
|
|
Format of input samplesheet |
|
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 |
|
format |
file-path |
|
|
A comma separated list of PGS score IDs, e.g. PGS000802 |
|
type |
string |
|
|
A comma separated list of PGS Catalog publications, e.g. PGP000001 |
|
type |
string |
|
|
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 |
|
|
A path to a directory that should contain relabelled genotypes |
|
type |
string |
|
default |
None |
|
format |
directory-path |
|
|
Path to the output directory where the results will be saved. |
|
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})$ |
Ancestry options#
type |
object |
|
default |
||
properties |
||
|
A YAML or JSON file that contains parameters for handling ancestry options |
|
type |
string |
|
default |
None |
|
|
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 |
Reference options#
Define how reference genomes are defined and processed
type |
object |
|
default |
||
properties |
||
|
Path to reference database. Must be set if –ref_samplesheet is not set. |
|
type |
string |
|
default |
None |
|
format |
file-path |
|
|
Path to a samplesheet that describes the structure of reference data. Must be set if –ref isn’t set. |
|
type |
string |
|
|
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 |
|
format |
file-path |
|
|
Exclude variants with missing call frequencies greater than a threshold (in reference genomes) |
|
type |
number |
|
maximum |
1 |
|
minimum |
0 |
|
default |
0.1 |
|
|
Exclude samples with missing call frequencies greater than a threshold (in reference genomes) |
|
type |
number |
|
maximum |
1 |
|
minimum |
0 |
|
default |
0.1 |
|
|
Exclude variants with allele frequency 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 |
1e-04 |
|
|
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 |
|
format |
file-path |
|
|
Path to a file that contains areas of high linkage disequilibrium in the reference data (build GRCh38). |
|
type |
string |
|
format |
file-path |
Compatibility options#
Define parameters that control how scoring files and target genomes are made compatible with each other
type |
object |
|
default |
||
properties |
||
|
A YAML or JSON file that contains parameters for handling compatibility options |
|
type |
string |
|
default |
None |
|
|
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 |
|
|
Enable fast matching, which significantly increases RAM usage (32GB minimum recommended) |
|
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 |
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|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 |
|
|
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 |
|
|
Directory to keep pipeline Nextflow logs and reports. |
|
type |
string |
|
default |
${params.outdir}/pipeline_info |
|
|
Boolean whether to validate parameters against the schema at runtime |
|
type |
boolean |
|
default |
True |
|
|
Show all params when using –help |
|
type |
boolean |
|
|
What platform is the pipeline executing on? |
|
type |
string |
|
enum |
amd64, arm64 |
|
default |
amd64 |
|
|
Enable parallel calculation of scores. This is I/O and RAM intensive. |
|
type |
boolean |