Merge branch 'develop' into feature/split-pbsv-call

PacificBiosciences · Oct 5, 2023 · 7156b6e · 7156b6e
2 parents 6b73fd3 + 85e8f98
commit 7156b6e
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Showing 3 changed files with 18 additions and 33 deletions.
diff --git a/workflows/cohort_analysis/inputs.json b/workflows/cohort_analysis/inputs.json
@@ -28,15 +28,10 @@
     },
     "hificnv_expected_bed_male": "File",
     "hificnv_expected_bed_female": "File",
-    "gnomad_af": "File",
-    "hprc_af": "File",
-    "gff": "File",
-    "population_vcfs": [
-      {
-        "data": "File",
-        "data_index": "File"
-      }
-    ]
+    "gnomad_af": "File? (optional)",
+    "hprc_af": "File? (optional)",
+    "gff": "File? (optional)",
+    "population_vcfs": "Array[WomCompositeType {\n data -> File\ndata_index -> File \n}]? (optional)"
   },
   "cohort_analysis.glnexus_mem_gb": "Int? (optional)",
   "cohort_analysis.pbsv_call_mem_gb": "Int? (optional)",

diff --git a/workflows/input_template.json b/workflows/input_template.json
@@ -7,8 +7,8 @@
         "movie_bams": "Array[File]",
         "sex": "String?",
         "affected": "Boolean",
-        "father_id": "String?",
-        "mother_id": "String?"
+        "father_id": "String? (optional)",
+        "mother_id": "String? (optional)"
       }
     ],
     "phenotypes": "Array[String]"
@@ -27,15 +27,10 @@
       },
     "hificnv_expected_bed_male": "File",
     "hificnv_expected_bed_female": "File",
-    "gnomad_af": "File",
-    "hprc_af": "File",
-    "gff": "File",
-    "population_vcfs": [
-      {
-        "data": "File",
-        "data_index": "File"
-      }
-    ]
+    "gnomad_af": "File? (optional)",
+    "hprc_af": "File? (optional)",
+    "gff": "File? (optional)",
+    "population_vcfs": "Array[WomCompositeType {\n data -> File\ndata_index -> File \n}]? (optional)"
   },
   "humanwgs.slivar_data": {
     "slivar_js": "File",
@@ -46,11 +41,11 @@
     "lof_lookup": "File",
     "clinvar_lookup": "File"
   },
-  "humanwgs.deepvariant_version": "String (optional)",
+  "humanwgs.deepvariant_version": "String? (optional)",
   "humanwgs.deepvariant_model": "WomCompositeType {\n model -> WomCompositeType {\n data -> File\ndata_index -> File \n}\nmetadata -> File \n}? (optional)",
-  "humanwgs.pbsv_call_mem_gb": "Int (optional)",
-  "humanwgs.glnexus_mem_gb": "Int (optional)",
-  "humanwgs.run_tertiary_analysis": "Boolean (optional, default = false)",
+  "humanwgs.pbsv_call_mem_gb": "Int? (optional)",
+  "humanwgs.glnexus_mem_gb": "Int? (optional)",
+  "humanwgs.run_tertiary_analysis": "Boolean? (optional, default = false)",
   "humanwgs.backend": "String ['GCP', 'Azure', 'AWS', or 'HPC']",
   "humanwgs.zones": "String? (optional); required if backend is set to 'GCP' or 'AWS'",
   "humanwgs.aws_spot_queue_arn": "String? (optional); required if backend is set to 'AWS'",

diff --git a/workflows/sample_analysis/inputs.json b/workflows/sample_analysis/inputs.json
@@ -21,15 +21,10 @@
     },
     "hificnv_expected_bed_male": "File",
     "hificnv_expected_bed_female": "File",
-    "gnomad_af": "File",
-    "hprc_af": "File",
-    "gff": "File",
-    "population_vcfs": [
-      {
-        "data": "File",
-        "data_index": "File"
-      }
-    ]
+    "gnomad_af": "File? (optional)",
+    "hprc_af": "File? (optional)",
+    "gff": "File? (optional)",
+    "population_vcfs": "Array[WomCompositeType {\n data -> File\ndata_index -> File \n}]? (optional)"
   },
   "sample_analysis.deepvariant_version": "String",
   "sample_analysis.deepvariant_model": "WomCompositeType {\n model -> WomCompositeType {\n data -> File\ndata_index -> File \n}\nmetadata -> File \n}? (optional)",