Resolve "Move inference to start of pipeline"

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PR checklist

• This comment contains a description of changes (with reason)
• If you've fixed a bug or added code that should be tested, add tests!
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• Close issue
  Closes #47 (closed)

/cc @ghenry @venkat.malladi

Moves metadata (species, endness, spike, stranded) to the start of the pipeline and does not use any user entered metadata for any downstream processes

workflow/conf/biohpc.config

@@ -3,34 +3,49 @@ process {
   queue = 'super'
   clusterOptions = '--hold'
 
-  withName:getBag {
+  withName: getBag {
     executor = 'local'
   }
-  withName:getData {
+  withName: getData {
     executor = 'local'
   }
-  withName:parseMetadata {
+  withName: parseMetadata {
     executor = 'local'
   }
-  withName:getRef {
+  withName: trimData {
+    queue = 'super'
+  }
+  withName: getRefInfer {
+    executor = 'local'
+  }
+  withName: downsampleData {
     executor = 'local'
   }
-  withName:trimData {
+  withName: alignSampleData {
+    queue = 'super'
+  }
+  withName: inferMetadata {
     queue = 'super'
   }
-  withName:alignData {
+  withName: getRef {
+    executor = 'local'
+  }
+  withName: alignData {
     queue = '256GB,256GBv1'
   }
   withName: dedupData {
     queue = 'super'
   }
-  withName:fastqc {
+  withName: countData {
+    queue = 'super'
+  }
+  withName: makeBigWig {
     queue = 'super'
   }
-  withName:inferMetadata {
+  withName: fastqc {
     queue = 'super'
   }
-  withName: makeBigWig {
+  withName: dataQC {
     queue = 'super'
   }
 }