update schema with support for --maf_target and --geno_miss_target

PGScatalog · Jul 30, 2024 · 351518e · 351518e
1 parent ad835ae
commit 351518e
Show file tree

Hide file tree

Showing 3 changed files with 208 additions and 153 deletions.
diff --git a/modules/local/ancestry/intersect_variants.nf b/modules/local/ancestry/intersect_variants.nf
@@ -33,8 +33,8 @@ process INTERSECT_VARIANTS {
     pgscatalog-intersect --ref $ref_variants \
         --target $variants \
         --chrom $meta.chrom \
-        --maf_target 0.1 \
-        --geno_miss 0.1 \
+        --maf_target $params.maf_target \
+        --geno_miss $params.geno_miss_target \
         --outdir . \
         -v
 

diff --git a/nextflow.config b/nextflow.config
@@ -43,6 +43,8 @@ params {
     n_popcomp = 5
     normalization_method = "empirical mean mean+var"
     n_normalization = 4
+    maf_target = 0.1
+    geno_miss_target = 0.1
 
     // compatibility params
     liftover = false