diff --git a/processing-for-variant-discovery-gatk3.wdl b/processing-for-variant-discovery-gatk3.wdl
index 7631ab9..56c05cc 100644
--- a/processing-for-variant-discovery-gatk3.wdl
+++ b/processing-for-variant-discovery-gatk3.wdl
@@ -76,18 +76,14 @@ workflow GenericPreProcessingWorkflow {
   # Align flowcell-level unmapped input bams in parallel
   scatter (unmapped_bam in flowcell_unmapped_bams) {
   
-    # Because of a wdl/cromwell bug this is not currently valid so we have to sub(sub()) in each task
-    # String base_name = sub(sub(unmapped_bam, "gs://.*/", ""), unmapped_bam_suffix + "$", "")
-
-    String sub_strip_path = "gs://.*/"
-    String sub_strip_unmapped = unmapped_bam_suffix + "$"
+    String base_name = sub(basename(unmapped_bam), unmapped_bam_suffix + "$", "") + ".unmerged"
 
     # Map reads to reference
     call SamToFastqAndBwaMem {
       input:
         input_bam = unmapped_bam,
         bwa_commandline = bwa_commandline,
-        output_bam_basename = sub(sub(unmapped_bam, sub_strip_path, ""), sub_strip_unmapped, "") + ".unmerged",
+        output_bam_basename = base_name,
         ref_fasta = ref_fasta,
         ref_fasta_index = ref_fasta_index,
         ref_dict = ref_dict,
@@ -108,7 +104,7 @@ workflow GenericPreProcessingWorkflow {
         bwa_commandline = bwa_commandline,
         bwa_version = GetBwaVersion.version,
         aligned_bam = SamToFastqAndBwaMem.output_bam,
-        output_bam_basename = sub(sub(unmapped_bam, sub_strip_path, ""), sub_strip_unmapped, "") + ".aligned.unsorted",
+        output_bam_basename = base_name,
         ref_fasta = ref_fasta,
         ref_fasta_index = ref_fasta_index,
         ref_dict = ref_dict,
@@ -120,7 +116,7 @@ workflow GenericPreProcessingWorkflow {
     call SortAndFixTags as SortAndFixReadGroupBam {
       input:
       input_bam = MergeBamAlignment.output_bam,
-      output_bam_basename = sub(sub(unmapped_bam, sub_strip_path, ""), sub_strip_unmapped, "") + ".sorted",
+      output_bam_basename = base_name,
       ref_dict = ref_dict,
       ref_fasta = ref_fasta,
       ref_fasta_index = ref_fasta_index,