add bdduk stats file for multiqc report

cwl/workflows/workflow_illumina_quality.cwl

@@ -190,8 +190,8 @@ steps:
       reference:
         valueFrom: "/unlock/references/databases/riboKmers.fa.gz"
       threads: threads
-      memory: memory    
-    out: [out_forward_reads, out_reverse_reads, summary]
+      memory: memory
+    out: [out_forward_reads, out_reverse_reads, summary, stats_file]
 
 #############################################
 #### Filter PhiX
@@ -217,7 +217,7 @@ steps:
         valueFrom: "/unlock/references/databases/phix.fasta"
       threads: threads
       memory: memory
-    out: [out_forward_reads, out_reverse_reads, summary]
+    out: [out_forward_reads, out_reverse_reads, summary, stats_file]
 
 #############################################
 #### Kraken2
@@ -308,7 +308,7 @@ steps:
     run: ../expressions/files_to_folder.cwl
     in:
       files:
-        source: [fastqc_illumina_before/html_files, fastqc_illumina_before/zip_files, fastqc_illumina_after/html_files, fastqc_illumina_after/zip_files, fastp/html_report, fastp/json_report, reference_filter_illumina/stats, reference_filter_illumina/covstats, reference_filter_illumina/log, illumina_quality_kraken2/sample_report, illumina_quality_kraken2_krona/krona_html, phix_filter/summary, rrna_filter/summary]
+        source: [fastqc_illumina_before/html_files, fastqc_illumina_before/zip_files, fastqc_illumina_after/html_files, fastqc_illumina_after/zip_files, fastp/html_report, fastp/json_report, reference_filter_illumina/stats, reference_filter_illumina/covstats, reference_filter_illumina/log, illumina_quality_kraken2/sample_report, illumina_quality_kraken2_krona/krona_html, phix_filter/summary, phix_filter/stats_file, rrna_filter/summary, rrna_filter/stats_file]
         linkMerge: merge_flattened
         pickValue: all_non_null
       step: step