left a trailing _

tasks/basecalling/task_dorado_demux.wdl

@@ -51,10 +51,10 @@ task dorado_demux {
       echo "Processing $fastq_file"
 
       if [[ "$fastq_file" == *"unclassified"* ]]; then
-        final_fastq="~{fastq_file_name}unclassified.fastq"
+        final_fastq="~{fastq_file_name}-unclassified.fastq"
       else
         barcode=$(echo "$fastq_file" | sed -E 's/.*_(barcode[0-9]+)\.fastq/\1/')
-        final_fastq="~{fastq_file_name}${barcode}.fastq"
+        final_fastq="~{fastq_file_name}-${barcode}.fastq"
       fi
 
       echo "Renaming $fastq_file to $final_fastq"
@@ -70,20 +70,20 @@ task dorado_demux {
     done
 
     echo "### Zipping all FASTQ files ###"
-    for fastq in ~{fastq_file_name}_*.fastq; do
+    for fastq in ~{fastq_file_name}-*.fastq; do
       echo "Zipping $fastq"
       gzip -f "$fastq"
     done
 
     echo "### Final FASTQ Files ###"
-    ls -lh ~{fastq_file_name}_*.fastq.gz || echo "No gzipped FASTQ files found."
+    ls -lh ~{fastq_file_name}-*.fastq.gz || echo "No gzipped FASTQ files found."
 
     echo "### Dorado demux process completed successfully ###"
     date
   >>>
 
   output {
-    Array[File] fastq_files = glob("~{fastq_file_name}*.fastq.gz")
+    Array[File] fastq_files = glob("~{fastq_file_name}-*.fastq.gz")
   }
 
    runtime {
@@ -92,4 +92,4 @@ task dorado_demux {
     memory: "~{memory} GB"
     disks: "local-disk ~{disk_size} SSD"
   }
-}
+}