# HG changeset patch
# User nate
# Date 1753810983 0
# Node ID c6a1b04e2f2b17a82cb2c4a39823b780a8eb673b
# Parent  b3d94db291c16d6cc263b2ca59892dd7ad176304
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 9758b72ead4e42804f77ff7166bf6f860c01de11

diff -r b3d94db291c1 -r c6a1b04e2f2b data_manager/hisat2_index_builder.xml
--- a/data_manager/hisat2_index_builder.xml	Tue Jul 29 17:09:29 2025 +0000
+++ b/data_manager/hisat2_index_builder.xml	Tue Jul 29 17:43:03 2025 +0000
@@ -26,7 +26,7 @@
 
         mkdir -p '${out_file.extra_files_path}' &&
         ln -s '${all_fasta_source.fields.path}' '${out_file.extra_files_path}/${fasta_file_name}' &&
-        working=$(pwd)` &&
+        working="\$(pwd)"` &&
         cd '${out_file.extra_files_path}' &&
 
         hisat2-build -p "\${GALAXY_SLOTS:-1}"