From 219eb433983b37b45cf35b0f621bfdea98253bd3 Mon Sep 17 00:00:00 2001 From: Nick Wiltsie Date: Wed, 17 Apr 2024 14:08:06 -0700 Subject: [PATCH] Apply all auto-fixes from shellcheck v0.9.0 (#14) --- modify_reference_path.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modify_reference_path.sh b/modify_reference_path.sh index 68b0c5a..4c3d7d1 100644 --- a/modify_reference_path.sh +++ b/modify_reference_path.sh @@ -3,10 +3,10 @@ refpath_default=$1 refpath_modified=$2 -cat ${refpath_default} | \ +cat "${refpath_default}" | \ sed 's|IMPUTEINFOFILE = \".*|IMPUTEINFOFILE = \"/opt/battenberg_reference/impute_info.txt\"|' | \ sed 's|G1000PREFIX = \".*|G1000PREFIX = \"/opt/battenberg_reference/1000_genomes_loci/1000_genomes_allele_index_chr\"|' | \ sed 's|G1000PREFIX_AC = \".*|G1000PREFIX_AC = \"/opt/battenberg_reference/1000_genomes_loci/1000_genomes_loci_chr\"|' | \ sed 's|GCCORRECTPREFIX = \".*|GCCORRECTPREFIX = \"/opt/battenberg_reference/1000_genomes_gcContent/1000_genomes_GC_corr_chr\"|' | \ sed 's|PROBLEMLOCI = \".*|PROBLEMLOCI = \"/opt/battenberg_reference/battenberg_problem_loci/probloci.txt.gz\"|' | \ - sed 's|REPLICCORRECTPREFIX = \".*|REPLICCORRECTPREFIX = \"/opt/battenberg_reference/battenberg_wgs_replication_timing_correction_1000_genomes/1000_genomes_replication_timing_chr\"|' > ${refpath_modified} + sed 's|REPLICCORRECTPREFIX = \".*|REPLICCORRECTPREFIX = \"/opt/battenberg_reference/battenberg_wgs_replication_timing_correction_1000_genomes/1000_genomes_replication_timing_chr\"|' > "${refpath_modified}"