From 1f585e2e3861a5d7e83e786268112f9d9c1b324e Mon Sep 17 00:00:00 2001 From: Andrew Green Date: Fri, 1 Sep 2023 14:00:02 +0100 Subject: [PATCH] Escapes for awk variables --- workflows/databases/rediportal.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/databases/rediportal.nf b/workflows/databases/rediportal.nf index 7ca3667d..94e72d73 100644 --- a/workflows/databases/rediportal.nf +++ b/workflows/databases/rediportal.nf @@ -23,7 +23,7 @@ process fetch_rediportal_bedfile { """ wget -O REDI_sorted_untabbed.bed $params.databases.rediportal.bed_remote - awk 'BEGIN {OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7}' REDI_sorted_untabbed.bed > REDI_sorted.bed + awk 'BEGIN {OFS="\t"} {print \$1,\$2,\$3,\$4,\$5,\$6,\$7} ' REDI_sorted_untabbed.bed > REDI_sorted.bed """ }