diff --git a/CHANGELOG.md b/CHANGELOG.md
index 02b87873590bf3057b5eeef49b958fcc09fd6885..94fb07f6f3eb71672da69fbcaced6e5deae18617 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,6 +10,7 @@ that users understand how the changes affect the new version.
 -->
 Version 3.1.0-dev
 ---------------------------
++ Lima: Remove outputPrefix variable from output section.
 + Isoseq3: Make sure stderr log file from Refine is unique and not overwritten.
 + Isoseq3: Add workaround in Refine for glob command not locating files in output directory.
 + Isoseq3: Fix --min-polya-length argument syntax.
diff --git a/lima.wdl b/lima.wdl
index 67d9ff278fe4d0afb805277ef91a2bffbb32c99e..619764fc4e5b408c94f23b73e962c657f8a50564 100644
--- a/lima.wdl
+++ b/lima.wdl
@@ -97,9 +97,9 @@ task Lima {
     }
 
     output {
-        Array[File] outputFLfile = glob("~{basename(outputPrefix)}*.bam")
-        Array[File] outputFLindexFile = glob("~{basename(outputPrefix)}*.bam.pbi")
-        Array[File] outputFLxmlFile = glob("~{basename(outputPrefix)}*.subreadset.xml")
+        Array[File] outputFLfile = glob("*.bam")
+        Array[File] outputFLindexFile = glob("*.bam.pbi")
+        Array[File] outputFLxmlFile = glob("*.subreadset.xml")
         File outputSTDERRfile = outputPrefix + ".fl.stderr.log"
         File outputJSONfile = outputPrefix + ".fl.json"
         File outputCountsFile = outputPrefix + ".fl.lima.counts"