use --force instead of --quiet to handle uncompressed data

PGScatalog · Aug 6, 2024 · 125d2f0 · 125d2f0
1 parent 3d0f516
commit 125d2f0
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/modules/local/plink2_score.nf b/modules/local/plink2_score.nf
@@ -64,7 +64,7 @@ process PLINK2_SCORE {
             $input ${geno.baseName} \
             --out ${output}
 
-        n_missing=\$(comm -3 <(zcat --quiet $scorefile | tail -n +2 | cut -f 1 | sort) <(sort ${output}.sscore.vars) | wc -l | tr -d ' ')
+        n_missing=\$(comm -3 <(zcat --force $scorefile | tail -n +2 | cut -f 1 | sort) <(sort ${output}.sscore.vars) | wc -l | tr -d ' ')
 
         if [ \$n_missing -gt 0 ]
         then
@@ -93,7 +93,7 @@ process PLINK2_SCORE {
             $input ${geno.baseName} \
             --out ${output}
 
-        n_missing=\$(comm -3 <(zcat --quiet $scorefile | tail -n +2 | cut -f 1 | sort) <(sort ${output}.sscore.vars) | wc -l | tr -d ' ')
+        n_missing=\$(comm -3 <(zcat --force $scorefile | tail -n +2 | cut -f 1 | sort) <(sort ${output}.sscore.vars) | wc -l | tr -d ' ')
 
         if [ \$n_missing -gt 0 ]
         then