From 125d2f0dd51b1b60f55af1f659129e724993fd3e Mon Sep 17 00:00:00 2001 From: Benjamin Wingfield Date: Tue, 6 Aug 2024 15:26:32 +0100 Subject: [PATCH] use --force instead of --quiet to handle uncompressed data --- modules/local/plink2_score.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/local/plink2_score.nf b/modules/local/plink2_score.nf index 2bf2cb7d..71bde2d1 100644 --- 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