Merge branch 'koeho006-master-patch-36622' into 'master'

Doc update

See merge request !1

cwl/workflows/workflow_metagenomics.cwl

@@ -13,8 +13,8 @@ doc: |
     Workflow for Metagenomics from raw reads to annotated bins.
     Steps:
       - workflow_quality.cwl:
-          FastQC (control)
-          fastp (trimming)
+          - FastQC (control)
+          - fastp (trimming)
       - Kraken2 (Taxonomic Read Classification
       - SPAdes (Assembly)
       - QUAST (Assembly quality report)
@@ -25,37 +25,45 @@ doc: |
       - SAPP (bin annotation)
 
 outputs:
-  x1:
+  fastqc_output:
     label: FASTQC
+    doc: Quality reporting by FASTQC
     type: Directory[]
     outputSource: workflow_quality/files_to_folder_fastqc
-  x2:
+  filter_output:
     label: Filtered reads
+    doc: Reads filtered output folder
     type: Directory[]
     outputSource: workflow_quality/files_to_folder_filtered
-  x3:
+  kraken2_output:
     label: KRAKEN2
+    doc: Classification output folder by kraken
     type: Directory
     outputSource: kraken_files_to_folder/results
-  x4:
+  spades_output:
     label: SPADES
+    doc: Metagenome assembly output by SPADES
     type: Directory
     outputSource: spades_files_to_folder/results
-  x5:
+  quast_output:
     label: QUAST
+    doc: Quast analysis output folder
     type: Directory
     outputSource: quast_files_to_folder/results
-  x6:
+  bam_output:
     label: BAM files
+    doc: Mapping results in indexed BAM format
     type: Directory
     outputSource: sorted_bam_files_to_folder/results
-  x7:
+  metabat2_output:
     label: MetaBat2
+    doc: MetaBat2 output directory
     type: Directory
     outputSource: metabat_files_to_folder/results
-  x8:
+  sapp_output:
     label: SAPP Genomes
     type: Directory
+    doc: Folder containing genomes annotated by SAPP 
     outputSource: sapp_files_to_folder/results
 
 inputs:
@@ -385,4 +393,4 @@ $namespaces:
   edam: http://edamontology.org/
 
 $schemas:
- - http://edamontology.org/EDAM_1.18.owl
\ No newline at end of file
+ - http://edamontology.org/EDAM_1.18.owl