Write consistent column sets to variant information files (#330)

* write only mandatory pvar columns * Fix samplesheet parsing error warnings (#322) * Update SamplesheetParser.groovy * fix multiple samplesheet error message --------- Co-authored-by: Benjamin Wingfield <[email protected]> --------- Co-authored-by: Sam Lambert <[email protected]>
PGScatalog · Jul 4, 2024 · cc3a26e · cc3a26e
1 parent ccfd636
commit cc3a26e
Show file tree

Hide file tree

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