as data subtypes are not to be exposed as facets, change "* Supplement" to dataTypes

Author: junjun-zhang

payload-gen-variant-calling/main.py

@@ -37,10 +37,10 @@
     'indel': ['Simple Nucleotide Variation', ['Raw InDel Calls', None], ['Pindel'], ['GATK:Mutect2']],
     'cnv': ['Copy Number Variation', ['Raw CNV Calls', None], ['ASCAT']],
     'sv': ['Structural Variation', ['Raw SV Calls', None], ['BRASS']],
-    'caveman-supplement': ['Simple Nucleotide Variation', ['Variant Calling Supplement', 'SNV Supplement'], ['CaVEMan']],
-    'pindel-supplement': ['Simple Nucleotide Variation', ['Variant Calling Supplement', 'InDel Supplement'], ['Pindel']],
-    'ascat-supplement': ['Copy Number Variation', ['Variant Calling Supplement', 'CNV Supplement'], ['ASCAT']],
-    'brass-supplement': ['Structural Variation', ['Variant Calling Supplement', 'SV Supplement'], ['BRASS']],
+    'caveman-supplement': ['Simple Nucleotide Variation', ['SNV Supplement', None], ['CaVEMan']],
+    'pindel-supplement': ['Simple Nucleotide Variation', ['InDel Supplement', None], ['Pindel']],
+    'ascat-supplement': ['Copy Number Variation', ['CNV Supplement', None], ['ASCAT']],
+    'brass-supplement': ['Structural Variation', ['SV Supplement', None], ['BRASS']],
     'timings-supplement': ['Quality Control Metrics', ['Analysis QC', 'Runtime Stats'], None, None],
     'bas_metrics': ['Quality Control Metrics', ['Aligned Reads QC', 'Alignment Metrics'], ['Sanger:bam_stats']],
     'contamination_metrics': ['Quality Control Metrics', ['Analysis QC', 'Cross Sample Contamination'], ['Sanger:verifyBamHomChk'], ['GATK:CalculateContamination']],

tests/data/66f84b1e-dad1-4981-916e-07e62ff53410.variant_calling_supplement.payload.json

@@ -66,7 +66,7 @@
       "fileAccess": "controlled",
       "info": {
         "data_category": "Simple Nucleotide Variation",
-        "data_subtype": "SNV Supplement",
+        "data_subtype": null,
         "analysis_tools": [
           "CaVEMan"
         ],
@@ -89,7 +89,7 @@
         ]
       },
       "fileName": "TEST-PR.DO250122.SA610148.wgs.20210414.sanger-wxs.somatic.caveman-supplement.tgz",
-      "dataType": "Variant Calling Supplement"
+      "dataType": "SNV Supplement"
     },
     {
       "fileType": "TGZ",
@@ -98,7 +98,7 @@
       "fileAccess": "controlled",
       "info": {
         "data_category": "Simple Nucleotide Variation",
-        "data_subtype": "InDel Supplement",
+        "data_subtype": null,
         "analysis_tools": [
           "Pindel"
         ],
@@ -118,7 +118,7 @@
         ]
       },
       "fileName": "TEST-PR.DO250122.SA610148.wgs.20210414.sanger-wxs.somatic.pindel-supplement.tgz",
-      "dataType": "Variant Calling Supplement"
+      "dataType": "InDel Supplement"
     }
   ],
   "workflow": {