Update output arguments

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

src/featurecounts/config.vsh.yaml

@@ -35,37 +35,35 @@ functionality:
 
     - name: Outputs
       arguments:
-        - name: --output
+        - name: --output_counts
           alternatives: ["-o"]
           type: file
           direction: output
           description: | 
-            Name of output file including read counts. A separate file including summary statistics of counting results is also included in the output ('<output>.summary'). Both files are in tab delimited format.
-          must_exist: true
-          example: features.txt
+            Name of output file including read counts in tab delimited format.
+          required: true
+          example: features.tsv
         - name: --output_summary
           type: file
           direction: output
           description: | 
-            Summary statistics of counting results is also included in the output ('<output>.summary'). 
-          must_exist: true
-          example: features.txt.summary
+            Summary statistics of counting results in tab delimited format.
+          required: false
+          example: summary.tsv
         - name: --output_junctions
           type: file
           direction: output
           description: | 
-            Count of number of reads supporting each exon-exon junction. See '--junctions' for more information.
-          must_exist: false
-          example: features.txt.jcounts
-          must_exist: false
-        - name: --r_path
+            Count of number of reads supporting each exon-exon junction. This file is only created if `--junctions` is specified.
+          example: junctions.txt
+          required: false
+        - name: --results_path
           type: file
           direction: output
           description: | 
-            Directory to save the detailed assignment results. If unspecified, the directory where counting results are saved is used. See -R for more format information.
-          must_exist: false
+            Directory to save the detailed assignment results. Use `--detailed_results_format` to determine the format of the detailed results.
           example: detailed_results/
-          must_exist: false
+          required: false
 
     - name: Annotation
       arguments: