optional ref filter + change order

cwl/workflows/workflow_illumina_quality.cwl

@@ -79,7 +79,7 @@ inputs:
     doc: Reverse sequence fastq file(s) locally
     label: Reverse reads
   filter_references:
-    type: string[]
+    type: string[]?
     doc: References fasta file(s) for filtering    
     label: Filter reference file(s)
     default: ["/unlock/references/databases/bbduk/GCA_000001405.28_GRCh38.p13_genomic.fna.gz"] # HUMAN
@@ -93,6 +93,11 @@ inputs:
     doc: Optionally run Kraken2
     label: Kraken2
     default: true
+  run_filter_references:
+    type: boolean?
+    doc: Optionally filter references
+    label: Filter References
+    default: false
   kraken_database:
     type: string?
     doc: Kraken2 database location
@@ -177,6 +182,53 @@ steps:
       deduplicate: deduplicate
       threads: threads
     out: [out_forward_reads, out_reverse_reads, html_report, json_report]
+
+#############################################
+#### rRNA filter
+  rrna_filter:
+    label: rRNA filter (bbduk)
+    doc: Filters rRNA sequences from reads using bbduk
+    when: $(inputs.filter_rrna)
+    run: ../bbmap/bbduk_filter.cwl
+    in:
+      identifier:
+        source: identifier
+        valueFrom: $(self+"_rRNA-filter")
+      filter_rrna: filter_rrna
+      forward_reads: reference_filter_illumina/out_forward_reads
+      reverse_reads: reference_filter_illumina/out_reverse_reads
+      reference:
+        valueFrom: "/unlock/references/databases/riboKmers.fa.gz"
+      threads: threads
+      memory: memory    
+    out: [out_forward_reads, out_reverse_reads, summary]
+
+#############################################
+#### Filter PhiX
+  phix_filter:
+    label: PhiX filter (bbduk)
+    doc: Filters illumina spike-in PhiX sequences from reads using bbduk
+    run: ../bbmap/bbduk_filter.cwl
+    in:
+      identifier:
+        source: identifier
+        valueFrom: $(self+"_illumina_filtered")
+      forward_reads:
+        source:
+        - rrna_filter/out_forward_reads
+        - reference_filter_illumina/out_forward_reads
+        pickValue: first_non_null
+      reverse_reads:
+        source:
+        - rrna_filter/out_reverse_reads
+        - reference_filter_illumina/out_reverse_reads
+        pickValue: first_non_null
+      reference:
+        valueFrom: "/unlock/references/databases/phix.fasta"
+      threads: threads
+      memory: memory
+    out: [out_forward_reads, out_reverse_reads, summary]
+
 #############################################
 #### Kraken2
   illumina_quality_kraken2:
@@ -189,8 +241,8 @@ steps:
         valueFrom: $(inputs.tmp_id)_unfiltered_illumina
       threads: threads
       database: kraken_database
-      forward_reads: fastp/out_forward_reads
-      reverse_reads: fastp/out_reverse_reads
+      forward_reads: phix_filter/out_forward_reads
+      reverse_reads: phix_filter/out_reverse_reads
       paired_end: 
         default: true
     out: [sample_report]
@@ -208,6 +260,7 @@ steps:
   combine_references: 
     label: Combine references
     doc: Combine references to a single fasta file
+    when: $(inputs.run_filter_references)
     run: ../bash/concatenate.cwl
     in:
       # infiles:
@@ -226,6 +279,7 @@ steps:
   reference_filter_illumina:
     label: Reference read mapping
     doc: Map reads against references using BBMap
+    when: $(inputs.run_filter_references)
     run: ../bbmap/bbmap_filter-reads.cwl
     in:
       identifier: identifier
@@ -237,52 +291,6 @@ steps:
       memory: memory
     out: [out_forward_reads, out_reverse_reads, log, stats, covstats]
 
-#############################################
-#### rRNA filter
-  rrna_filter:
-    label: rRNA filter (bbduk)
-    doc: Filters rRNA sequences from reads using bbduk
-    when: $(inputs.filter_rrna)
-    run: ../bbmap/bbduk_filter.cwl
-    in:
-      identifier:
-        source: identifier
-        valueFrom: $(self+"_rRNA-filter")
-      filter_rrna: filter_rrna
-      forward_reads: reference_filter_illumina/out_forward_reads
-      reverse_reads: reference_filter_illumina/out_reverse_reads
-      reference:
-        valueFrom: "/unlock/references/databases/riboKmers.fa.gz"
-      threads: threads
-      memory: memory    
-    out: [out_forward_reads, out_reverse_reads, summary]
-
-#############################################
-#### Filter PhiX
-  phix_filter:
-    label: PhiX filter (bbduk)
-    doc: Filters illumina spike-in PhiX sequences from reads using bbduk
-    run: ../bbmap/bbduk_filter.cwl
-    in:
-      identifier:
-        source: identifier
-        valueFrom: $(self+"_illumina_filtered")
-      forward_reads:
-        source:
-        - rrna_filter/out_forward_reads
-        - reference_filter_illumina/out_forward_reads
-        pickValue: first_non_null
-      reverse_reads:
-        source:
-        - rrna_filter/out_reverse_reads
-        - reference_filter_illumina/out_reverse_reads
-        pickValue: first_non_null
-      reference:
-        valueFrom: "/unlock/references/databases/phix.fasta"
-      threads: threads
-      memory: memory
-    out: [out_forward_reads, out_reverse_reads, summary]
-
 #############################################
 #### FASTQC
   fastqc_illumina_after: