accept multiple kraken2 databases and run them seperately

cwl/workflows/workflow_illumina_quality.cwl

@@ -10,13 +10,13 @@ requirements:
 label: Illumina read quality control, trimming and contamination filter. 
 doc: | 
   **Workflow for Illumina paired read quality control, trimming and filtering.**<br />
-  Multiple read pairs will be merged into single paired dataset.<br />
+  Multiple paired datasets will be merged into single paired dataset.<br />
   Summary:
   - FastQC on raw data files<br />
   - fastp for read quality trimming<br />
-  - Kraken2 for taxonomic classification of reads<br />
-  - BBduk for phix and rRNA filtering<br />
-  - BBmap for (contamination) filtering using given references<br />
+  - BBduk for phiX and (optional) rRNA filtering<br />
+  - Kraken2 for taxonomic classification of reads (optional)<br />
+  - BBmap for (contamination) filtering using given references (optional)<br />
   - FastQC on filtered (merged) data<br />
 
   **All tool CWL files and other workflows can be found here:**<br>
@@ -89,10 +89,10 @@ inputs:
     label: Deduplicate reads
     default: false
   kraken_database:
-    type: string?
+    type: string[]?
     doc: Kraken2 database location
     label: Kraken2 database
-    default: "/unlock/references/databases/Kraken2/K2_PlusPF_20210517"
+    default: ["/unlock/references/databases/Kraken2/K2_PlusPF_20210517"]
   
   keep_reference_mapped_reads:
     type: boolean
@@ -185,8 +185,8 @@ steps:
         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
+      forward_reads: fastp/out_forward_reads
+      reverse_reads: fastp/out_reverse_reads
       reference:
         valueFrom: "/unlock/references/databases/riboKmers.fa.gz"
       threads: threads
@@ -226,10 +226,11 @@ steps:
     doc: Taxonomic classification of FASTQ reads
     when: $(inputs.kraken_database !== null)
     run: ../kraken2/kraken2.cwl
+    scatter: database
     in:
       tmp_id: identifier
       identifier:
-        valueFrom: $(inputs.tmp_id)_unfiltered_illumina
+        valueFrom: $(inputs.tmp_id)_Qfiltered
       threads: threads
       kraken_database: kraken_database
       database: kraken_database
@@ -244,6 +245,7 @@ steps:
     doc: Visualization of Kraken2 classification with Krona
     when: $(inputs.kraken_database !== null)
     run: ../krona/krona.cwl
+    scatter: kraken
     in:
       kraken_database: kraken_database
       kraken: illumina_quality_kraken2/sample_report