--- a/bionano_scaffold.xml	Tue May 25 20:12:52 2021 +0000
+++ b/bionano_scaffold.xml	Sat May 29 15:58:03 2021 +0000
@@ -55,9 +55,9 @@
         -f
         $zip_file
         -o ./
-        && cat $output_file_NCBI $output_file_not_scaffolded > total_contigs_raw.fasta
         #if $trim_cut_sites
-            && python '$__tool_directory__/remove_fake_cut_sites.py' 'total_contigs_raw.fasta' 'total_contigs_trimmed.fasta' 'output.log'
+            && python '$__tool_directory__/remove_fake_cut_sites.py' $output_file_NCBI 'SCAFFOLD_NCBI_trimmed.fasta' 'output.log'
+            && python '$__tool_directory__/remove_fake_cut_sites.py' $output_file_not_scaffolded 'NOT_SCAFFOLDED_trimmed.fasta' 'output.log'
         #end if        
     ]]>    </command>
     <configfiles>
@@ -420,22 +420,26 @@
         -->
     </inputs>
     <outputs>
-        <data name="ngs_contigs" format="fasta" from_work_dir="total_contigs_raw.fasta" label="${tool.name} on ${on_string}: NGScontigs">
+        <data name="ngs_contigs_scaffold" format="fasta" from_work_dir="hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD_NCBI.fasta" label="${tool.name} on ${on_string}: NGScontigs scaffold NCBI">
             <filter>trim_cut_sites == False</filter>
         </data>
-        <data name="ngs_contigs_trimmed" format="fasta" from_work_dir="total_contigs_trimmed.fasta" label="${tool.name} on ${on_string}: NGScontigs trimmed">
+        <data name="ngs_contigs_not_scaffolded" format="fasta" from_work_dir="hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD_NOT_SCAFFOLDED.fasta" label="${tool.name} on ${on_string}: NGScontigs not scaffolded">
+            <filter>trim_cut_sites == False</filter>
+        </data>
+        <data name="ngs_contigs_scaffold_trimmed" format="fasta" from_work_dir="SCAFFOLD_NCBI_trimmed.fasta" label="${tool.name} on ${on_string}: NGScontigs scaffold NCBI trimmed">
             <filter>trim_cut_sites</filter>
         </data>
-        <data name="ngs_contigs_trimmed_report" format="txt" from_work_dir="output.log" label="${tool.name} on ${on_string}: NGScontigs trimmed log">
+        <data name="ngs_contigs_not_scaffolded_trimmed" format="fasta" from_work_dir="NOT_SCAFFOLDED_trimmed.fasta" label="${tool.name} on ${on_string}: NGScontigs not scaffolded trimmed">
             <filter>trim_cut_sites</filter>
         </data>
         <data name="report" format="txt" from_work_dir="hybrid_scaffolds/hybrid_scaffold_informatics_report.txt" label="${tool.name} on ${on_string}: hybrid scaffold report"/>
+        <data name="conflicts" format="txt" from_work_dir="hybrid_scaffolds/conflicts.txt" label="${tool.name} on ${on_string}: conflicts"/>
         <data name="results" format="zip" from_work_dir="results.zip" label="${tool.name} on ${on_string}: results">
             <filter>zip_file</filter>
         </data>
     </outputs>
     <tests>
-        <test expect_num_outputs="3">
+        <test expect_num_outputs="5">
             <param name="ngs_fasta" value="assembly.fasta.gz"/>
             <param name="bionano_cmap" value="colormap_assembly.cmap"/>
             <param name="conflict_filter_genome" value="3"/>
@@ -446,12 +450,24 @@
             </conditional>
             <param name="zip_file" value="true"/>
             <param name="trim_cut_sites" value="false"/>
-            <output name="ngs_contigs" ftype="fasta">
+            <output name="ngs_contigs_scaffold" ftype="fasta">
                 <assert_contents>
-                    <has_size value="4753369" delta="300" />
+                    <has_size value="4753369" delta="100" />
+                    <has_n_lines n="2"/>
+                    <has_line line=">Super-Scaffold_1"/>
+                </assert_contents>
+            </output>
+            <output name="ngs_contigs_not_scaffolded" ftype="fasta">
+                <assert_contents>
+                    <has_size value="0"/>
                 </assert_contents>
             </output>
             <output name="report" file="test_01_report.txt" ftype="txt"/>
+            <output name="conflicts" ftype="txt">
+                <assert_contents>
+                    <has_text text="alignmentOrientation" />
+                </assert_contents>
+            </output>            
             <output name="results" ftype="zip">
                 <assert_contents>
                     <!--<has_size value="4231746" delta="300" />-->
@@ -474,7 +490,7 @@
                 <has_text text="hybridScaffold"/>
             </assert_stdout>
         </test>
-        <test expect_num_outputs="2">
+        <test expect_num_outputs="4">
             <param name="ngs_fasta" value="assembly.fasta.gz"/>
             <param name="bionano_cmap" value="colormap_assembly.cmap"/>
             <param name="conflict_filter_genome" value="2"/>
@@ -484,15 +500,24 @@
                 <param name="configuration" value="file"/>
                 <param name="configuration_file" value="configuration.xml"/>
             </conditional>
-            <output name="ngs_contigs" ftype="fasta">
+            <output name="ngs_contigs_scaffold" ftype="fasta">
                 <assert_contents>
                     <has_size value="4753369" delta="100" />
                     <has_n_lines n="2"/>
                     <has_line line=">Super-Scaffold_1"/>
                 </assert_contents>
             </output>
+            <output name="ngs_contigs_not_scaffolded" ftype="fasta">
+                <assert_contents>
+                    <has_size value="0"  />
+                </assert_contents>
+            </output>
             <output name="report" file="test_02_report.txt" ftype="txt"/>
-            <assert_stdout>
+            <output name="conflicts" ftype="txt">
+                <assert_contents>
+                    <has_text text="alignmentOrientation" />
+                </assert_contents>
+            </output>            <assert_stdout>
                 <has_text text='attr="maxmem" val0="8"'/>
             </assert_stdout>
             <assert_stdout>
@@ -509,7 +534,7 @@
                 <!--attribute_is path="hybridScaffold/global/flag[@attr='maxthreads']" attribute="val0" text="2"/-->
             </assert_stdout>
         </test>
-        <test expect_num_outputs="3">
+        <test expect_num_outputs="5">
             <param name="ngs_fasta" value="assembly.fasta.gz"/>
             <param name="bionano_cmap" value="colormap_assembly.cmap"/>
             <param name="conflict_filter_genome" value="2"/>
@@ -520,14 +545,24 @@
             </conditional>
             <param name="zip_file" value="true"/>
             <param name="trim_cut_sites" value="false"/>
-            <output name="ngs_contigs" ftype="fasta">
+            <output name="ngs_contigs_scaffold" ftype="fasta">
                 <assert_contents>
                     <has_size value="4753369" delta="100" />
                     <has_n_lines n="2"/>
                     <has_line line=">Super-Scaffold_1"/>
                 </assert_contents>
             </output>
+            <output name="ngs_contigs_not_scaffolded" ftype="fasta">
+                <assert_contents>
+                    <has_size value="0"/>
+                </assert_contents>
+            </output>
             <output name="report" file="test_03_report.txt" ftype="txt"/>
+            <output name="conflicts" ftype="txt">
+                <assert_contents>
+                    <has_text text="alignmentOrientation" />
+                </assert_contents>
+            </output>            
             <output name="results" ftype="zip">
                 <assert_contents>
                     <!--<has_size value="4231908" delta="300" />-->
@@ -550,7 +585,7 @@
                 <has_text text="hybridScaffold"/>
             </assert_stdout>
         </test>
-        <test expect_num_outputs="3">
+        <test expect_num_outputs="5">
             <param name="ngs_fasta" value="assembly.fasta.gz"/>
             <param name="bionano_cmap" value="colormap_assembly.cmap"/>
             <param name="conflict_filter_genome" value="2"/>
@@ -561,14 +596,24 @@
             </conditional>
             <param name="zip_file" value="true"/>
             <param name="trim_cut_sites" value="false"/>
-            <output name="ngs_contigs" ftype="fasta">
+            <output name="ngs_contigs_scaffold" ftype="fasta">
                 <assert_contents>
                     <has_size value="4753369" delta="100" />
                     <has_n_lines n="2"/>
                     <has_line line=">Super-Scaffold_1"/>
                 </assert_contents>
             </output>
+            <output name="ngs_contigs_not_scaffolded" ftype="fasta">
+                <assert_contents>
+                    <has_size value="0"/>
+                </assert_contents>
+            </output>
             <output name="report" file="test_04_report.txt" ftype="txt"/>
+            <output name="conflicts" ftype="txt">
+                <assert_contents>
+                    <has_text text="alignmentOrientation" />
+                </assert_contents>
+            </output>
             <output name="results" ftype="zip">
                 <assert_contents>
                     <has_archive_member path=".*/status.txt"/>
@@ -590,7 +635,7 @@
                 <has_text text="hybridScaffold"/>
             </assert_stdout>
         </test>
-        <test expect_num_outputs="3">
+        <test expect_num_outputs="4">
             <param name="ngs_fasta" value="assembly.fasta.gz"/>
             <param name="bionano_cmap" value="colormap_assembly.cmap"/>
             <param name="conflict_filter_genome" value="3"/>
@@ -600,16 +645,23 @@
                 <param name="configuration_file" value="configuration.xml"/>
             </conditional>
             <param name="trim_cut_sites" value="true"/>
-            <output name="ngs_contigs_trimmed" ftype="fasta">
+            <output name="ngs_contigs_scaffold_trimmed" ftype="fasta">
                 <assert_contents>
-                    <has_size value="4832591" delta="300" />
+                    <has_size value="4832591" delta="100" />
+                    <has_n_lines n="79224"/>
+                    <has_line line=">Super-Scaffold_1"/>
                 </assert_contents>
             </output>
-            <output name="ngs_contigs_trimmed_report" ftype="txt">
+            <output name="ngs_contigs_not_scaffolded_trimmed" ftype="fasta">
                 <assert_contents>
                     <has_size value="0" />
                 </assert_contents>
             </output>
+            <output name="conflicts" ftype="txt">
+                <assert_contents>
+                    <has_text text="alignmentOrientation" />
+                </assert_contents>
+            </output>            
             <output name="report" file="test_05_report.txt" ftype="txt"/>
             <assert_stdout>
                 <has_text text='attr="maxmem" val0="8"'/>