write only mandatory pvar columns

PGScatalog · Jul 1, 2024 · b0fb148 · b0fb148
1 parent ca334fa
commit b0fb148
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/modules/local/plink2_relabelpvar.nf b/modules/local/plink2_relabelpvar.nf
@@ -51,7 +51,7 @@ process PLINK2_RELABELPVAR {
         --set-all-var-ids '@:#:\$r:\$a' \\
         $set_ma_missing \\
         --pfile ${geno.baseName} $compressed \\
-        --make-just-pvar zs \\
+        --make-just-pvar zs cols="-xheader,-maybequal,-maybefilter,-maybeinfo,-maybecm" \\
         --out $output
 
     # -a: cross platform (mac, linux) method of preserving symlinks

diff --git a/modules/local/plink2_vcf.nf b/modules/local/plink2_vcf.nf
@@ -50,7 +50,7 @@ process PLINK2_VCF {
         $args \\
         --vcf $vcf $dosage_options \\
         --allow-extra-chr $chrom_filter \\
-        --make-pgen vzs \\
+        --make-pgen vzs pvar-cols="-xheader,-maybequal,-maybefilter,-maybeinfo,-maybecm" \\
         --out ${output}
 
     gzip ${output}.vmiss