--- a/cfsan_bettercallsal.xml	Mon Jul 15 11:01:13 2024 -0400
+++ b/cfsan_bettercallsal.xml	Mon Jul 15 11:20:22 2024 -0400
@@ -36,7 +36,7 @@
 	$__tool_directory__/0.7.0/cpipes
     --pipeline bettercallsal
     --input \${input_path}
-	--output \${pwd_path}/cpipes-output
+	--output cpipes-output
     --fq_suffix '${input_read_type_cond.fq_suffix}'
     #if (str($input_read_type_cond.input_read_type) == "single_long"):
         --fq_single_end true
@@ -59,8 +59,8 @@
 	--fq_filename_delim_idx $fq_filename_delim_idx
 	-profile gxkubernetes;
     mv './cpipes-output/bettercallsal-multiqc/multiqc_report.html' './multiqc_report.html' || exit 1;
-    rm -rf ./cpipes-output > || exit 1;
-    rm -rf ./work || exit 1
+    rm -rf ./cpipes-output || exit 1;
+    rm -rf ./work || exit 1;
     ]]></command>
     <inputs>
         <conditional name="input_read_type_cond">