diff --git a/tools/varvamp/macros.xml b/tools/varvamp/macros.xml
index cc2b54039f8..673a98c00c4 100644
--- a/tools/varvamp/macros.xml
+++ b/tools/varvamp/macros.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">1.2.0</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@TOOL_VERSION@">1.2.1</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <xml name="main_parameters">
         <conditional name="main_params">
             <param name="specify_how" type="select" label="How to set the main parameters, threshold for consensus nucleotides and max ambiguous nts per primer?">
diff --git a/tools/varvamp/test-data/ambiguous_consensus.fasta b/tools/varvamp/test-data/ambiguous_consensus.fasta
index 520c4a17c37..4ade916e0b0 100644
--- a/tools/varvamp/test-data/ambiguous_consensus.fasta
+++ b/tools/varvamp/test-data/ambiguous_consensus.fasta
@@ -1,2 +1,2 @@
->ambiguous_consensus
+>varVAMP_consensus
 tatcccgtrtycaractgayatccttattaayytgatgcaaccycgrcagcttgtkttccgrccygaagtyytstggaaycayccgatccagcgrgtyatacataatgagctggagcartactgccgwgcycgygctggycgytgyctkgargtkggsgcycayccaagatcyatyaatgayaacccyaatgtyytgcaccggtgcttyctycgcccggtyggdagagaygtmcagcgytggtaytcygccccsacycgyggyccagcggcyaaytgccgccgytcygcgctacgyggyytgccccctgtcgaycgyacmtaytgcttcgacgggttytcccgctgcgcytttgccgctgagacyggratygctttataytcactrcatgacctytggccytcggaygtygcggaggcya
diff --git a/tools/varvamp/test-data/test1.log b/tools/varvamp/test-data/test1.log
index 60b61464baf..8ee4eb3f611 100644
--- a/tools/varvamp/test-data/test1.log
+++ b/tools/varvamp/test-data/test1.log
@@ -33,3 +33,27 @@ PRIMER_MAX_BASE_PENALTY = 10
 PRIMER_3_PENALTY = (32, 16, 8, 4, 2)
 PRIMER_PERMUTATION_PENALTY = 0.1
 
+PROGRESS
+
Job:	 Checking config. 
+Result:	 config file passed
+
Job:	 Preprocessing alignment and cleaning gaps. 
+Result:	 0 gaps with 0 nucleotides
+
Job:	 Creating consensus sequences. 
+Result:	 length of the consensus is 420 nt
+
Job:	 Finding primer regions. 
+Result:	 92.6 % of the consensus sequence will be evaluated for primers
+
Job:	 Digesting into kmers. 
+Result:	 1245 kmers
+
Job:	 Filtering for primers. 
+Result:	 74 fw and 92 rv potential primers
+
Job:	 Considering primers with low penalties. 
+Result:	 10 fw and 13 rv primers
+
Job:	 Finding potential amplicons. 
+Result:	 17 potential amplicons
+
Job:	 Finding amplicons with low penalties. 
+Result:	 1 amplicons.
+
Job:	 Finalizing output. 
+Result:	 all done 
+
+
varVAMP 1.2.1 finished in 1.303803 sec!
+2024-10-18 11:03:39.364906
diff --git a/tools/varvamp/test-data/test2.log b/tools/varvamp/test-data/test2.log
index 50e450250d1..81d74370bfa 100644
--- a/tools/varvamp/test-data/test2.log
+++ b/tools/varvamp/test-data/test2.log
@@ -35,3 +35,27 @@ PRIMER_MAX_BASE_PENALTY = 10
 PRIMER_3_PENALTY = (32, 16, 8, 4, 2)
 PRIMER_PERMUTATION_PENALTY = 0.1
 
+PROGRESS
+
Job:	 Checking config. 
+Result:	 config file passed
+
Job:	 Preprocessing alignment and cleaning gaps. 
+Result:	 0 gaps with 0 nucleotides
+
Job:	 Creating consensus sequences. 
+Result:	 length of the consensus is 420 nt
+
Job:	 Finding primer regions. 
+Result:	 100.0 % of the consensus sequence will be evaluated for primers
+
Job:	 Digesting into kmers. 
+Result:	 2783 kmers
+
Job:	 Filtering for primers. 
+Result:	 265 fw and 310 rv potential primers
+
Job:	 Considering primers with low penalties. 
+Result:	 24 fw and 21 rv primers
+
Job:	 Finding potential amplicons. 
+Result:	 90 potential amplicons
+
Job:	 Creating amplicon scheme. 
+Result:	 99.52 % total coverage with 2 amplicons
+
Job:	 Finalizing output. 
+Result:	 all done 
+
+
varVAMP 1.2.1 finished in 2.13504 sec!
+2024-10-18 11:04:18.175094
diff --git a/tools/varvamp/test-data/test3.log b/tools/varvamp/test-data/test3.log
index 6a06b6989e0..45d42b9b1b4 100644
--- a/tools/varvamp/test-data/test3.log
+++ b/tools/varvamp/test-data/test3.log
@@ -39,7 +39,32 @@ QPROBE_GC_END = (0, 4)
 QPRIMER_DIFF = 2
 QPROBE_TEMP_DIFF = (5, 10)
 QPROBE_DISTANCE = (4, 15)
+END_OVERLAP = 5
 QAMPLICON_LENGTH = (70, 200)
 QAMPLICON_GC = (40, 60)
 QAMPLICON_DEL_CUTOFF = 4
 
+PROGRESS
+
Job:	 Checking config. 
+Result:	 config file passed
+
Job:	 Preprocessing alignment and cleaning gaps. 
+Result:	 0 gaps with 0 nucleotides
+
Job:	 Creating consensus sequences. 
+Result:	 length of the consensus is 420 nt
+
Job:	 Finding primer regions. 
+Result:	 71.0 % of the consensus sequence will be evaluated for primers
+
Job:	 Digesting into kmers. 
+Result:	 1084 kmers
+
Job:	 Filtering for primers. 
+Result:	 67 fw and 82 rv potential primers
+
Job:	 Finding qPCR probes. 
+Result:	 100 potential qPCR probes
+
Job:	 Finding unique amplicons with probe. 
+Result:	 3 unique amplicons with internal probe
+
Job:	 Filtering amplicons for deltaG. 
+Result:	 1 non-overlapping qPCR schemes that passed deltaG cutoff
+
Job:	 Finalizing output. 
+Result:	 all done 
+
+
varVAMP 1.2.1 finished in 4.028311 sec!
+2024-10-18 11:05:01.961908
diff --git a/tools/varvamp/test-data/test4.log b/tools/varvamp/test-data/test4.log
index 00137479bd6..c215a1c4b91 100644
--- a/tools/varvamp/test-data/test4.log
+++ b/tools/varvamp/test-data/test4.log
@@ -33,3 +33,27 @@ PRIMER_MAX_BASE_PENALTY = 10
 PRIMER_3_PENALTY = (32, 16, 8, 4, 2)
 PRIMER_PERMUTATION_PENALTY = 0.1
 
+PROGRESS
+
Job:	 Checking config. 
+Result:	 config file passed
+
Job:	 Preprocessing alignment and cleaning gaps. 
+Result:	 0 gaps with 0 nucleotides
+
Job:	 Creating consensus sequences. 
+Result:	 length of the consensus is 420 nt
+
Job:	 Finding primer regions. 
+Result:	 92.6 % of the consensus sequence will be evaluated for primers
+
Job:	 Digesting into kmers. 
+Result:	 1245 kmers
+
Job:	 Filtering for primers. 
+Result:	 88 fw and 107 rv potential primers
+
Job:	 Considering primers with low penalties. 
+Result:	 12 fw and 14 rv primers
+
Job:	 Finding potential amplicons. 
+Result:	 21 potential amplicons
+
Job:	 Finding amplicons with low penalties. 
+Result:	 1 amplicons.
+
Job:	 Finalizing output. 
+Result:	 all done 
+
+
varVAMP 1.2.1 finished in 1.407113 sec!
+2024-10-18 11:05:42.858771
diff --git a/tools/varvamp/varvamp.xml b/tools/varvamp/varvamp.xml
index cf329fcb98d..c72dd69f9d7 100644
--- a/tools/varvamp/varvamp.xml
+++ b/tools/varvamp/varvamp.xml
@@ -8,7 +8,7 @@
     </xrefs>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">varvamp</requirement>
-        <requirement type="package" version="2.0.1">primer3-py</requirement>
+        <requirement type="package" version="2.0.3">primer3-py</requirement>
         <requirement type="package" version="0.7.17">seqfold</requirement>
     </requirements>
     <version_command>varvamp --version</version_command>
@@ -53,7 +53,7 @@ results/
 #end if
 #if $mode.m_select == 'tiled' and $mode.scheme_outputs and 'primer_dimers' in $mode.scheme_outputs:
   ## ensure the unsolvable_primer_dimers.tsv file, which varVAMP creates only conditionally, exists in all cases, in which we try to discover it as an output
-  && cp -n dimers_fallback.tsv results/unsolvable_primer_dimers.tsv
+  && cp --update=none dimers_fallback.tsv results/unsolvable_primer_dimers.tsv
 #end if
     ]]></command>
     <configfiles>
@@ -283,7 +283,7 @@ $line]]></configfile>
             </output>
             <output name="primers_bed" ftype="bed">
                 <assert_contents>
-                    <has_n_lines n="2" />
+                    <has_n_lines n="3" />
                 </assert_contents>
             </output>
             <output name="amplicons_bed" ftype="bed">
@@ -299,8 +299,8 @@ $line]]></configfile>
             </output>
             <output name="primer_seqs" ftype="fasta">
                 <assert_contents>
-                    <has_line line=">AMPLICON_0_LEFT"/>
-                    <has_line line=">AMPLICON_0_RIGHT"/>
+                    <has_line line=">varVAMP_0_LEFT"/>
+                    <has_line line=">varVAMP_0_RIGHT"/>
                     <has_n_lines n="4"/>
                 </assert_contents>
             </output>
@@ -321,7 +321,7 @@ $line]]></configfile>
             <output name="varvamp_log" ftype="txt" compare="contains" file="test2.log" />
             <output name="primers_bed" ftype="bed">
                 <assert_contents>
-                    <has_n_lines n="4" />
+                    <has_n_lines n="5" />
                 </assert_contents>
             </output>
             <output name="amplicons_bed" ftype="bed">
@@ -371,7 +371,7 @@ $line]]></configfile>
             <output name="varvamp_log" ftype="txt" compare="contains" file="test3.log" />
             <output name="primers_bed" ftype="bed">
                 <assert_contents>
-                    <has_n_lines n="3" />
+                    <has_n_lines n="4" />
                 </assert_contents>
             </output>
             <output name="amplicons_bed" ftype="bed">
@@ -381,9 +381,9 @@ $line]]></configfile>
             </output>
             <output name="primer_seqs" ftype="fasta">
                 <assert_contents>
-                    <has_line line=">QPCR_SCHEME_0_PROBE"/>
-                    <has_line line=">QPCR_SCHEME_0_LEFT"/>
-                    <has_line line=">QPCR_SCHEME_0_RIGHT"/>
+                    <has_line line=">varVAMP_0_PROBE"/>
+                    <has_line line=">varVAMP_0_LEFT"/>
+                    <has_line line=">varVAMP_0_RIGHT"/>
                     <has_n_lines n="6"/>
                 </assert_contents>
             </output>