Configuration Guide¶

trait2gene configuration is YAML backed by strict Pydantic validation.

Minimum required fields¶

project
trait
input.sumstats
input.genome_build
input.ancestry
output.outdir

Example templates¶

Use these bundled templates as starting points:

src/trait2gene/data/examples/config.realpaths.template.yaml
src/trait2gene/data/examples/config.precomputed.template.yaml
src/trait2gene/data/examples/config.minimal.yaml

Common path fields¶

These usually need explicit absolute paths in production:

input.sumstats
resources.magma_bin
resources.reference_panel
resources.gene_locations
resources.gene_annotation
resources.feature_matrix_prefix
resources.raw_feature_dir
resources.precomputed_magma_prefix
resources.control_features_path
resources.subset_features_path
analysis.prioritization.locus_file
output.outdir

Prefix semantics¶

Some config entries are prefixes rather than single files.

`resources.reference_panel`¶

This must point to a PLINK prefix. If the prefix is:

/data/reference/1000g/eas/g1000_eas

then these files must exist:

/data/reference/1000g/eas/g1000_eas.bed
/data/reference/1000g/eas/g1000_eas.bim
/data/reference/1000g/eas/g1000_eas.fam

`resources.precomputed_magma_prefix`¶

This must point to a MAGMA prefix with:

.genes.out
.genes.raw

`resources.feature_matrix_prefix`¶

This must point to the prefix written by the upstream feature munging step, including:

.rows.txt
.cols.*.txt
.mat.*.npy

Modes¶

`standard`¶

Use this when you want the most guided experience:

external MAGMA execution
pre-munged feature bundle
standard output layout

`advanced`¶

Use this when you need to supply custom resources such as:

precomputed MAGMA outputs
raw feature directories
custom y_path
custom locus files

Upstream-aligned defaults¶

PoPS settings default to:

method = ridge
use_magma_covariates = true
use_magma_error_cov = true
remove_hla = true