diff --git a/tools/halfdeep/halfdeep.xml b/tools/halfdeep/halfdeep.xml
index 2d410223564..be55c582957 100644
--- a/tools/halfdeep/halfdeep.xml
+++ b/tools/halfdeep/halfdeep.xml
@@ -9,37 +9,35 @@
         ## Set up the directory structure expected by bam_depth.sh and halfdeep.sh
         ## See: https://github.com/makovalab-psu/HalfDeep?tab=readme-ov-file#expected-directory-layout
         ##
-        #import re
+        mkdir -p reads halfdeep/ref/mapped_reads &&
         ##
         ## reference
         ##
         ln -s '$ref' 'ref.$ref.ext' &&
-        touch ref.idx &&
+        #if not $mapped_reads
+            minimap2 -x map-pb -d ref.idx 'ref.$ref.ext' &&
+        #else
+            touch ref.idx &&
+        #end if
         ##
         ## reads
         ##
-        #set $reads_dir = "reads"
-        #set $mapped_reads_dir = "halfdeep/ref/mapped_reads"
-        mkdir -p '$reads_dir' '$mapped_reads_dir' &&
-        #for $read in $reads
-            #set $read_base = re.sub('[^\w\-\s]', '_', str($read.element_identifier))
-            ln -s '$read' '$reads_dir/${read_base}.$read.ext' &&
-            echo '$reads_dir/${read_base}.$read.ext' >> input.fofn &&
-            ##
-            ## mapped reads
-            ##
-            #for $mapped_read in $mapped_reads
-                ln -s '$mapped_read' "$mapped_reads_dir/${read_base}.bam" &&
-                ln -s "${read_base}.bam" "$mapped_reads_dir/${read_base}.sort.bam" &&
-                ln -s '$mapped_read.metadata.bam_index' "$mapped_reads_dir/${read_base}.sort.bam.bai" &&
-            #end for
-        #end for
+        #import re
+        #set $reads_base = re.sub('[^\w\-\s]', '_', str($reads.element_identifier))
+        ln -s '$reads' 'reads/${reads_base}.$reads.ext' &&
+        echo 'reads/${reads_base}.$reads.ext' >> input.fofn &&
+        ##
+        ## mapped reads
+        ##
+        #if $mapped_reads
+            ln -s '$mapped_reads' 'halfdeep/ref/mapped_reads/${reads_base}.bam' &&
+            ln -s '${reads_base}.bam' 'halfdeep/ref/mapped_reads/${reads_base}.sort.bam' &&
+            ln -s '$mapped_reads.metadata.bam_index' 'halfdeep/ref/mapped_reads/${reads_base}.sort.bam.bai' &&
+        #end if
         ##
         ## run bam_depth.sh
         ##
-        #for $line_number in range(1, len($reads) + 1)
-            bam_depth.sh 'ref.$ref.ext' $line_number &&
-        #end for
+        bam_depth.sh 'ref.$ref.ext' 1 &&
         ##
         ## run halfdeep.sh
         ##
@@ -47,23 +45,22 @@
     ]]></command>
     <inputs>
         <param name="ref" type="data" format="fasta,fasta.gz" label="Genome Assembly" help="A Genome Assembly in FASTA format."/>
-        <param name="reads" type="data" format="fastqsanger,fastqsanger.bz2,fastqsanger.gz" multiple="true" label="Sequencing Reads" help="Sequencing Reads for the Genome Assembly in FASTQ format."/>
-        <param name="mapped_reads" type="data" format="bam" multiple="true" label="Aligned Reads" help="Alignments of the Sequencing Reads to the Genome Assembly in BAM format."/>
+        <param name="reads" type="data" format="fastqsanger,fastqsanger.gz" label="Sequencing Reads" help="Sequencing Reads for the Genome Assembly in FASTQ format."/>
+         <param name="mapped_reads" type="data" format="bam" value="" optional="true" label="Aligned Reads" help="Alignments of the Sequencing Reads to the Genome Assembly in BAM format."/>
     </inputs>
     <outputs>
-        <data name="scaffold_len" format="tabular" from_work_dir="halfdeep/ref/scaffold_lengths.dat" label="Scaffold lengths for ${on_string}"/>
-        <data name="depth_dat" format="tabular.gz" from_work_dir="halfdeep/ref/depth.dat.gz" label="Depth for ${on_string}"/>
-        <data name="pct_cmds" format="text" from_work_dir="halfdeep/ref/percentile_commands.sh" label="Percentile to value for ${on_string}"/>
         <data name="halfdeep_dat" format="bed" from_work_dir="halfdeep/ref/halfdeep.dat" label="HalfDeep on ${on_string}"/>
     </outputs>
     <tests>
-        <test expect_num_outputs="4">
+        <test expect_num_outputs="1">
             <param name="ref" value="ref.fasta.gz" ftype="fasta.gz"/>
             <param name="reads" value="reads.fasta.gz" ftype="fasta.gz"/>
             <param name="mapped_reads" value="mapped_reads.bam" ftype="bam"/>
-            <output name="scaffold_len" file="scaffold_lengths.tabular" ftype="tabular"/>
-            <output name="depth_dat" file="depth.tabular.gz" ftype="tabular.gz"/>
-            <output name="pct_cmds" file="percentile.txt" ftype="text"/>
+            <output name="halfdeep_dat" file="halfdeep.bed" ftype="bed"/>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="ref" value="ref.fasta.gz" ftype="fasta.gz"/>
+            <param name="reads" value="reads.fasta.gz" ftype="fasta.gz"/>
             <output name="halfdeep_dat" file="halfdeep.bed" ftype="bed"/>
         </test>
     </tests>
@@ -71,11 +68,11 @@
 
 HalfDeep identifies genomic regions with half-depth coverage based on sequencing read mappings. These regions may reveal insights into heterogametic sex chromosomes, haplotype-specific variation, or potential assembly errors such as heterotypic duplications.
 
-Given the following three inputs:
+Given the following inputs:
 
 1. A genome assembly in FASTA format.
 2. Reads in FASTQ format.
-3. Mapped reads in BAM format
+3. Mapped reads in BAM format (optional)
 
 HalfDeep automates the following tasks:
 
@@ -83,14 +80,11 @@ HalfDeep automates the following tasks:
 2. Calculating per-base read depth.
 3. Smoothing read coverage using a defined window with genodsp.
 4. Determining the percentile of read coverage.
-5. Identifying genomic regions with half-depth coverage based on a specified percentile threshold (e.g., 40–60%) and exporting them in BED file forma
+5. Identifying genomic regions with half-depth coverage based on a specified percentile threshold (e.g., 40–60%) and exporting them in BED file format
 
-HalfDeep produces the following outputs:
+HalfDeep produces the following output:
 
-1. Scaffold lengths: A tabular file containing the name and legth of each sequence in the genome assembly.
-2. Depths: A tabular file containing the read depts.
-3. A tabular file containing the name and legth of each sequence in the genome assembly: stuff
-4. HalfDeep: BED file containina regions of the genome assembly that are "covered at half depth"
+1. HalfDeep: BED file containing regions of the genome assembly that are "covered at half depth"
     ]]></help>
     <expand macro="citations"/>
 </tool>
diff --git a/tools/halfdeep/test-data/depth.tabular.gz b/tools/halfdeep/test-data/depth.tabular.gz
deleted file mode 100644
index 9d7edfed841..00000000000
Binary files a/tools/halfdeep/test-data/depth.tabular.gz and /dev/null differ
diff --git a/tools/halfdeep/test-data/percentile.txt b/tools/halfdeep/test-data/percentile.txt
deleted file mode 100644
index 6bc9e16a101..00000000000
--- a/tools/halfdeep/test-data/percentile.txt
+++ /dev/null
@@ -1,6 +0,0 @@
-export percentile40=0.975
-export percentile50=0.986
-export percentile60=1.331
-export halfPercentile40=0.4875
-export halfPercentile50=0.493
-export halfPercentile60=0.6655
diff --git a/tools/halfdeep/test-data/scaffold_lengths.tabular b/tools/halfdeep/test-data/scaffold_lengths.tabular
deleted file mode 100644
index 151e87d25f8..00000000000
--- a/tools/halfdeep/test-data/scaffold_lengths.tabular
+++ /dev/null
@@ -1,3 +0,0 @@
-FAKE1	482501
-FAKE2	366529
-FAKE3	150970