change kraken.cwl version and busco fix

cwl/workflows/workflow_nanopore_assembly.cwl

@@ -185,10 +185,10 @@ steps:
     out: [standard_report, sample_report]
 
   illumina_kraken2:
-    label: Kraken2 workflow
-    doc: Read taxonomic classification using the Kraken2
+    label: Taxonomic classification with Kraken2
+    doc: Taxonomic classification of FASTQ reads
     when: $(inputs.binning)
-    run: ../metagenomics/kraken2/kraken2.cwl
+    run: ../kraken2/kraken2.cwl
     in:
       binning: binning
       tmp_id: identifier
@@ -198,26 +198,29 @@ steps:
       database: kraken_database
       forward_reads: workflow_quality_illumina/QC_forward_reads
       reverse_reads: workflow_quality_illumina/QC_forward_reads
-    out: [report, kraken]
-#############################################
-#### Gzip compression of kraken2 files
+      paired_end: 
+        default: true
+    out: [standard_report, sample_report]
+
   kraken2_compress:
     run: ../bash/pigz.cwl
+    label: Compress kraken2
+    doc: Compress large kraken2 report file 
     scatter: inputfile
     in:
-      inputfile: [nanopore_kraken2/standard_report, illumina_kraken2/kraken]
+      inputfile: [nanopore_kraken2/standard_report, illumina_kraken2/standard_report]
       threads: threads
     out: [outfile]
-#############################################
-#### Visual representation of taxonomic classification
+
   kraken2_krona:
-    label: taxonomic classification visualization
-    doc: visualization of taxonomic classification with Krona
+    label: Krona Kraken2
+    doc: Visualization of kraken2 with Krona
     run: ../krona/krona.cwl
     scatter: kraken
     in:
-      kraken: [nanopore_kraken2/sample_report, illumina_kraken2/report]
+      kraken: [nanopore_kraken2/sample_report, illumina_kraken2/sample_report]
     out: [krona_html]
+
 #############################################
 #### De novo assembly with Flye
   flye:
@@ -255,7 +258,7 @@ steps:
 #### Workflow Pilon assembly polishing
   workflow_pilon:
     label: Pilon
-    doc: Short reads assembly polishing with Pilon
+    doc: Illumina reads assembly polishing with Pilon
     when: $(inputs.binning)
     run: workflow_pilon_mapping.cwl
     in:
@@ -273,7 +276,7 @@ steps:
 #### Assembly evaluation with QUAST
   metaquast_nanopore_pilon:
     label: Illumina assembly evaluation
-    doc: Illumina evaluation of polished assembly with metaQUAST
+    doc: Illumina evaluation of pilon polished assembly with metaQUAST
     when: $(inputs.binning)
     run: ../metaquast/metaquast.cwl
     in:
@@ -284,8 +287,8 @@ steps:
 #############################################
 #### BBmap read mapping (illumina reads) for binning
   illumina_pilon_readmapping:
-    label: BBmap read mapping
-    doc: Illumina read mapping using BBmap on assembled contigs
+    label: Read mapping
+    doc: Illumina read mapping on pilon assembly for binning
     when: $(inputs.binning)
     run: ../bbmap/bbmap.cwl
     in:
@@ -326,7 +329,7 @@ steps:
       threads: threads
       step: 
         default: 1
-    out: [metabat2_output,checkm_output,gtdbtk_output]
+    out: [metabat2_output,checkm_output,gtdbtk_output,busco_output]
 
 #############################################    
 #### Move to folder if not part of a workflow
@@ -336,7 +339,7 @@ steps:
     run: ../expressions/files_to_folder.cwl
     in:
       files:
-        source: [kraken2_compress/outfile, nanopore_kraken2/sample_report, kraken2_krona/krona_html, illumina_kraken2/report]
+        source: [kraken2_compress/outfile, kraken2_krona/krona_html, nanopore_kraken2/sample_report, illumina_kraken2/sample_report]
         linkMerge: merge_flattened
       destination:
         valueFrom: $("2_Kraken2_classification")
@@ -470,7 +473,7 @@ steps:
     in:
       binning: binning
       folders:
-        source: [workflow_binning/metabat2_output, workflow_binning/checkm_output, workflow_binning/gtdbtk_output]
+        source: [workflow_binning/metabat2_output, workflow_binning/checkm_output, workflow_binning/gtdbtk_output, workflow_binning/busco_output]
         linkMerge: merge_flattened
         pickValue: all_non_null
       destination: