Update src/busco/config.vsh.yaml

Co-authored-by: Robrecht Cannoodt <[email protected]>

src/busco/config.vsh.yaml

@@ -39,20 +39,41 @@ functionality:
 
     - name: Outputs
       arguments:
-        - name: --output_dir
-          alternatives: ["-o"]
-          required: true
+        - name: --short_summary_json
+          required: false
           direction: output
           type: file
+          example: short_summary.json
           description: |
-            Path to output directory for publishing BUSCO results
-          example: output
-        - name: --output_prefix
-          type: string
+            Output file for short summary in JSON format.
+        - name: --short_summary_txt
+          required: false
+          direction: output
+          type: file
+          example: short_summary.txt
+          description: |
+            Output file for short summary in TXT format.
+        - name: --full_table
           required: false
+          direction: output
+          type: file
+          example: full_table.tsv
+          description: |
+            Full table output in TSV format.
+        - name: --missing_list
+          required: false
+          direction: output
+          type: file
+          example: missing_list.tsv
+          description: |
+            Missing list output in TSV format.
+        - name: --output_dir
+          required: false
+          direction: output
+          type: file
+          example: output_dir/
           description: |
-            Name of the analysis run, output folders and files will be labeled with this name. if not specified the output will be the input file name."
-          example: busco_protein
+            The full output directory, if so desired.
 
     - name: Resource and Run Settings
       arguments: