--- a/cfsan_centriflaken.xml	Tue Jul 02 16:53:12 2024 -0400
+++ b/cfsan_centriflaken.xml	Wed Jul 03 10:45:24 2024 -0400
@@ -8,7 +8,7 @@
 	mkdir -p cpipes-input || exit 1;
     pwd_path=\$(pwd);
     time_stamp=\$(date +%Y-%m-%d-%s);
-    work_dir="\${pwd_path}/centriflaken_work_dir-"\${time_stamp};
+    work_dir="/galaxy/nf-work-dirs/centriflaken_work_dir-"\${time_stamp};
     mkdir -p \$work_dir || exit 1;
     #import re
     #if (str($input_read_type_cond.input_read_type) == "single_long"):
@@ -38,6 +38,7 @@
     #end if
 	$__tool_directory__/0.4.2/cpipes
     --pipeline $input_read_type_cond.pipeline_cond.pipeline
+    -work-dir \${work_dir}
     #if ($input_read_type_cond.pipeline_cond.pipeline == "centriflaken"):
         --fq_single_end true
         --flye_genome_size '${genome_size}'