--- a/cfsan_centriflaken.xml	Thu Aug 04 10:39:37 2022 -0400
+++ b/cfsan_centriflaken.xml	Thu Aug 04 10:45:55 2022 -0400
@@ -34,7 +34,7 @@
 	        ln -sf '$pair.reverse' './cpipes-input/$read_R2';
 	    #end for
     #end if
-	$__tool_directory__/0.3.0/cpipes
+	$__tool_directory__/0.4.0/cpipes
     --pipeline $input_read_type_cond.pipeline_cond.pipeline
     #if ($input_read_type_cond.pipeline_cond.pipeline == "centriflaken"):
         --fq_single_end true
@@ -66,6 +66,9 @@
 	--fq_filename_delim '${fq_filename_delim}'
 	--fq_filename_delim_idx $fq_filename_delim_idx
 	--centrifuge_extract_bug '${centrifuge_extract_bug}'
+    #if ($input_read_type_cond.pipeline_cond.rm_dup_seqs == "true"):
+        --seqkit_rmdup_run true
+    #end if
 	-profile kondagac;
     mv './cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-multiqc/multiqc_report.html' './multiqc_report.html' > /dev/null 2>&1 || exit 1;
     mv './cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-results/kraken2_extract_contigs' kraken2_extract_contigs > /dev/null 2>&1 || exit 1;
@@ -102,6 +105,11 @@
                             help="THIS OPTION IS IGNORED IF THE INPUT READS ARE SHORT READS.">
                                 <option value="NA" selected="true">N/A</option>
                         </param>
+                        <param name="rm_dup_seqs" type="select" label="Remove duplicate sequences"
+                            help="Selecting yes will compare sequence content and remove identical sequences i.e. only the first occured sequence record will be saved.">
+                            <option value="true">yes</option>
+                            <option value="false" selected="true">no</option>
+                        </param>
                     </when>
                 </conditional>
                 <param name="fq_suffix" value=".fastq.gz" type="text" label="Suffix of the Unpaired FASTQ"/>
@@ -118,6 +126,11 @@
                             help="THIS OPTION IS IGNORED IF THE INPUT READS ARE SHORT READS.">
                                 <option value="NA" selected="true">N/A</option>
                         </param>
+                        <param name="rm_dup_seqs" type="select" label="Remove duplicate sequences"
+                            help="Selecting yes will compare sequence content and remove identical sequences i.e. only the first occured sequence record will be saved.">
+                            <option value="true">yes</option>
+                            <option value="false" selected="true">no</option>
+                        </param>
                     </when>
                 </conditional>
                 <param name="fq_suffix" value="_R1_001.fastq.gz" type="text" label="Suffix of the R1 FASTQ"/>