Apply all auto-fixes from shellcheck v0.9.0 (#14)

uclahs-cds · Apr 17, 2024 · 219eb43 · 219eb43
1 parent 25412d9
commit 219eb43
Showing 1 changed file with 2 additions and 2 deletions.
diff --git 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}"