Hs metrics

modules.json

@@ -80,6 +80,16 @@
                         "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
                         "installed_by": ["modules"]
                     },
+                    "picard/collecthsmetrics": {
+                        "branch": "master",
+                        "git_sha": "0ce3ab0ac301f160225b22254fa238478b4389f2",
+                        "installed_by": ["modules"]
+                    },
+                    "picard/createsequencedictionary": {
+                        "branch": "master",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "installed_by": ["modules"]
+                    },
                     "picard/markduplicates": {
                         "branch": "master",
                         "git_sha": "eca65aa4a5e2e192ac44d6962c8f9260f314ffb8",

nextflow.config

@@ -22,8 +22,11 @@ params {
     multiqc_logo               = null
     max_multiqc_email_size     = '25.MB'
     multiqc_methods_description = null
-
-
+
+    // HS metrics
+    target_intervals    = null
+    bait_intervals      = null 
+
     // Intermediate files
     save_reference             = false
     save_align_intermeds       = false

nextflow_schema.json

@@ -637,5 +637,21 @@
         {
             "$ref": "#/definitions/institutional_config_options"
         }
-    ]
+    ],
+    "properties": {
+        "target_intervals": {
+            "type": "string",
+            "default": "None",
+            "hidden": true,
+            "description": "Path to BED file with Target intervals"
+        },
+        "bait_intervals": {
+            "type": "string",
+            "default": "None",
+            "hidden": true,
+            "description": "Path to Bed file with Bait intervals"
+        }
+    }
 }
+
+