--- a/pima_report.xml	Thu Apr 20 18:10:58 2023 +0000
+++ b/pima_report.xml	Thu Apr 20 18:47:01 2023 +0000
@@ -7,7 +7,11 @@
     <command detect_errors="exit_code"><![CDATA[
 #import re
 
-#set analysis_name = re.sub('[^\s\w\-]', '_', str($fastq_file.element_identifier))
+#if str($read_type) == 'ont':
+    #set analysis_name = re.sub('[^\s\w\-]', '_', str($fastq_file.element_identifier))
+#else:
+    #set analysis_name = re.sub('[^\s\w\-]', '_', str($extracted_fastq_file.element_identifier))
+#end if
 #set assembly_name = re.sub('[^\s\w\-]', '_', str($assembly_fasta_file.element_identifier))
 
 #if str($bedtools_complementbed_file) not in ['None', '']:
@@ -137,6 +141,7 @@
         <param name="contig_coverage_file" type="data" format="tabular,tsv" label="Contig coverage tabular file"/>
         <param name="dnadiff_snps_file" type="data" format="tabular" label="DNAdiff snps tabular file"/>
         <param name="errors_file" type="data" format="txt" label="AMR mutation regions error txt file"/>
+        <param name="extracted_fastq_file" type="data" format="fastqsanger,fastqsanger.gz" optional="true" label="Fastq sample file extracted from a paired collection" help="Used only with Illumina paired reads, leave blank to ignore"/>
         <param name="fastq_file" type="data" format="fastqsanger,fastqsanger.gz" label="Fastq sample file"/>
         <param name="features_bed" format="bed" type="data_collection" collection_type="list" label="Collection of best feature hits BED files"/>
         <param name="features_png" format="png" type="data_collection" collection_type="list" label="Collection of best feature hits PNG files"/>