--- a/trimmomatic.xml	Sun Jan 14 11:00:33 2024 +0000
+++ b/trimmomatic.xml	Wed Jan 24 08:56:01 2024 +0000
@@ -120,15 +120,15 @@
          <option value="pair_of_files">Paired-end (two separate input files)</option>
          <option value="collection">Paired-end (as collection)</option>
       </param>
-    <when value="se">
-      <param name="fastq_in" type="data" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz" label="Input FASTQ file" />
-    </when>
-    <when value="pair_of_files">
-      <param name="fastq_r1_in" type="data" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz"
-         label="Input FASTQ file (R1/first of pair)" />
-      <param name="fastq_r2_in" type="data" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz"
-         label="Input FASTQ file (R2/second of pair)" />
-    </when>
+      <when value="se">
+        <param name="fastq_in" type="data" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz" label="Input FASTQ file" />
+      </when>
+      <when value="pair_of_files">
+        <param name="fastq_r1_in" type="data" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz"
+          label="Input FASTQ file (R1/first of pair)" />
+        <param name="fastq_r2_in" type="data" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz"
+          label="Input FASTQ file (R2/second of pair)" />
+      </when>
       <when value="collection">
         <param name="fastq_pair" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz" type="data_collection" collection_type="paired" label="Select FASTQ dataset collection with R1/R2 pair" />
       </when>
@@ -222,19 +222,19 @@
     <param name="output_err" type="boolean" label="Output trimmomatic log messages?" truevalue="yes" falsevalue="no" checked="False" help="these are the messages written to stderr (eg. for use in MultiQC)" />
   </inputs>
   <outputs>
-    <data name="fastq_out_r1_paired" label="${tool.name} on ${readtype.fastq_r1_in.name} (R1 paired)" format_source="fastq_r1_in">
+    <data name="fastq_out_r1_paired" default_identifier_source="readtype|fastq_r1_in" label="${tool.name} on ${readtype.fastq_r1_in.name} (R1 paired)" format_source="fastq_r1_in">
       <filter>readtype['single_or_paired'] == "pair_of_files"</filter>
     </data>
-    <data name="fastq_out_r2_paired" label="${tool.name} on ${readtype.fastq_r2_in.name} (R2 paired)" format_source="fastq_r2_in">
+    <data name="fastq_out_r2_paired" default_identifier_source="readtype|fastq_r2_in" label="${tool.name} on ${readtype.fastq_r2_in.name} (R2 paired)" format_source="fastq_r2_in">
       <filter>readtype['single_or_paired'] == "pair_of_files"</filter>
     </data>
-    <data name="fastq_out_r1_unpaired" label="${tool.name} on ${readtype.fastq_r1_in.name} (R1 unpaired)" format_source="fastq_r1_in">
+    <data name="fastq_out_r1_unpaired" default_identifier_source="readtype|fastq_r1_in" label="${tool.name} on ${readtype.fastq_r1_in.name} (R1 unpaired)" format_source="fastq_r1_in">
       <filter>readtype['single_or_paired'] == "pair_of_files"</filter>
     </data>
-    <data name="fastq_out_r2_unpaired" label="${tool.name} on ${readtype.fastq_r2_in.name} (R2 unpaired)" format_source="fastq_r2_in">
+    <data name="fastq_out_r2_unpaired" default_identifier_source="readtype|fastq_r2_in" label="${tool.name} on ${readtype.fastq_r2_in.name} (R2 unpaired)" format_source="fastq_r2_in">
       <filter>readtype['single_or_paired'] == "pair_of_files"</filter>
     </data>
-    <data name="fastq_out" label="${tool.name} on ${readtype.fastq_in.name}" format_source="fastq_in">
+    <data name="fastq_out" default_identifier_source="readtype|fastq_in" label="${tool.name} on ${readtype.fastq_in.name}" format_source="fastq_in">
       <filter>readtype['single_or_paired'] == 'se'</filter>
     </data>
     <collection name="fastq_out_paired" type="paired" label="${tool.name} on ${on_string}: paired">
@@ -242,10 +242,10 @@
       <data name="forward" label="${tool.name} on ${readtype.fastq_pair.forward.name} (R1 paired)" format_source="fastq_pair['forward']"/>
       <data name="reverse" label="${tool.name} on ${readtype.fastq_pair.reverse.name} (R2 paired)" format_source="fastq_pair['reverse']"/>
     </collection>
-      <collection name="fastq_out_unpaired" type="paired" label="${tool.name} on ${on_string}: unpaired">
-        <filter>readtype['single_or_paired'] == "collection"</filter>
-        <data name="forward" label="${tool.name} on ${readtype.fastq_pair.forward.name} (R1 unpaired)" format_source="fastq_pair['forward']"/>
-        <data name="reverse" label="${tool.name} on ${readtype.fastq_pair.reverse.name} (R2 unpaired)" format_source="fastq_pair['reverse']"/>
+    <collection name="fastq_out_unpaired" type="paired" label="${tool.name} on ${on_string}: unpaired">
+      <filter>readtype['single_or_paired'] == "collection"</filter>
+      <data name="forward" label="${tool.name} on ${readtype.fastq_pair.forward.name} (R1 unpaired)" format_source="fastq_pair['forward']"/>
+      <data name="reverse" label="${tool.name} on ${readtype.fastq_pair.reverse.name} (R2 unpaired)" format_source="fastq_pair['reverse']"/>
     </collection>
     <data name="log_file" format="txt" label="${tool.name} on ${on_string} (trimlog file)" from_work_dir="trimlog">
       <filter>output_logs</filter>