--- a/cfsan_centriflaken.xml	Wed Jun 29 23:40:53 2022 -0400
+++ b/cfsan_centriflaken.xml	Thu Jun 30 12:34:34 2022 -0400
@@ -37,6 +37,9 @@
 	--input \${pwd_path}/cpipes-input
 	--output \${pwd_path}/cpipes-output
     --fq_suffix '${fq_suffix}'
+    #if ($fq_filter_by_len > 0):
+        --fq_filter_by_len $fq_filter_by_len
+    #end if
 	--fq_filename_delim '${fq_filename_delim}'
 	--fq_filename_delim_idx $fq_filename_delim_idx
 	--centrifuge_extract_bug '${centrifuge_extract_bug}'
@@ -67,6 +70,8 @@
             <option value="pacbio_hifi">PacBio HiFi reads (&lt;1% error)</option>
         </param>
         <param name="fq_suffix" value=".fastq.gz" type="text" label="Suffix of the R1 FASTQ or Unpaired FASTQ"/>
+        <param name="fq_filter_by_len" value="" type="integer" label="Enter minimum read length to retain before starting the analysis"
+            help="Keep this option empty to use default values. Default for centriflaken (long reads) is 4000 bp and for centriflaken_hy (short reads) is 75 bp)"/>
         <param name="fq2_suffix" value="_R2_001.fastq.gz" type="text" label="Suffix of the R2 FASTQ R2"/>
         <param name="fq_filename_delim" type="text" value="_" label="File name delimitor by which samples are grouped together (--fq_filename_delim)" 
             help="This is the delimitor by which samples are grouped together to display in the final MultiQC report. For example, if your input data sets are mango_replicate1.fastq.gz, mango_replicate2.fastq.gz, orange_replicate1_maryland.fastq.gz, orange_replicate2_maryland.fastq.gz, then to create 2 samples mango and orange, the value for --fq_filename_delim would be _ (underscore) and the value for --fq_filename_delim_idx would be 1, since you want to group by the first word (i.e. mango or orange) after splitting the filename based on _ (underscore)"/>