--- a/varvamp.xml	Thu Oct 24 18:10:50 2024 +0000
+++ b/varvamp.xml	Thu Feb 13 09:20:17 2025 +0000
@@ -50,11 +50,6 @@
 '$alignment'
 results/
 
-#if $mode.scheme_outputs and 'primer_binding_sites' in $mode.scheme_outputs:
-  ## the leading header line written by this version of the tool
-  ## is less than helpful in that in can cause parsing issues with downstream tools like ivar trim
-  && tail -n +2 results/primers.bed > results/primers_headerless.bed
-#end if
 #if $mode.m_select == 'qpcr' and $mode.scheme_outputs and 'primer_seqs' in $mode.scheme_outputs:
   ## make the primer sequences fasta discoverable under the same name that is used in "single" mode
   && mv results/oligos.fasta results/primers.fasta
@@ -154,7 +149,7 @@
                 <param argument="--name" type="text" value="TILED_SCHEME" label="Name your primer scheme" help="This name will be used in various outputs of the tool." />
                 <expand macro="main_parameters" />
                 <expand macro="amplicon_length_restrictions" />
-                <param argument="--overlap" type="integer" min="1" value="100" label="Minimal required overlap between tiled amplicons" help="default: 100" />
+                <param argument="--overlap" type="integer" min="1" value="100" label="Minimal required overlap between tiled amplicon inserts" help="default: 100" />
                 <expand macro="blast_options" />
                 <expand macro="customize_advanced" />
                 <expand macro="primer_scheme_outputs">
@@ -224,7 +219,7 @@
             <data name="pool1_sequences" format="fasta" from_work_dir="results/primers_pool_1.fasta" label="${tool.name} on ${on_string}: Sequences of designed pool 1 primers" />
             <data name="pool2_sequences" format="fasta" from_work_dir="results/primers_pool_2.fasta" label="${tool.name} on ${on_string}: Sequences of designed pool 2 primers" />
         </collection>
-        <data name="primers_bed" format="bed" from_work_dir="results/primers_headerless.bed" label="${tool.name} on ${on_string}: Primer binding sites">
+        <data name="primers_bed" format="bed" from_work_dir="results/primers.bed" label="${tool.name} on ${on_string}: Primer binding sites">
             <filter>mode['scheme_outputs'] and 'primer_binding_sites' in mode['scheme_outputs']</filter>
         </data>
         <data name="amplicons_bed" format="bed" from_work_dir="results/amplicons.bed" label="${tool.name} on ${on_string}: Amplicon locations">
@@ -327,7 +322,7 @@
                 </conditional>
                 <param name="opt_length" value="150"/>
                 <param name="max_length" value="300"/>
-                <param name="overlap" value="100"/>
+                <param name="overlap" value="76"/>
             </conditional>
             <output name="varvamp_log" ftype="txt" compare="contains" file="test2.log" />
             <output name="primers_bed" ftype="bed">