Metadata output update

Cumulative update focused on metadata output:

• Add read length: both submitter entered and inferred (median length)
• Add calculated read counts: both raw and assigned
• Add median TIN
• Output multiqc json (for future use)
• Convert gene symbols to Entrez ID: for data-hub convenience (use version specific metadata - added to references)
• Create bash script to initiate parallel replicate runs from study RID
• Change consistence tests for assigned reads exact match to being within +/- 1/100,000 of expected

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!
• Documentation in docs is updated
• Replace dag.png with the most recent CI pipleine integrated_pe artifact
• CHANGELOG.md is updated
• README.md is updated
• LICENSE.md is updated with new contributors
• Docker images moved to production release and changed in pipeline
• Docker images used in the CI unit tests match those used in pipeline

• Close issue
  Closes #52 (closed) Closes #56 (closed)

/cc @ghenry @venkat.malladi

workflow/rna-seq.nf

@@ -842,7 +842,7 @@ process countData {
   output:
     path ("*.countTable.csv") into counts
     path ("*.countData.summary") into countsQC
-    path ("assignedReads") into inferMetadata_assignedReads
+    path ("assignedReads.csv") into inferMetadata_assignedReads
 
   script:
     """
@@ -888,7 +888,7 @@ process countData {
 // Extract number of assigned reads metadata into channel
 assignedReadsInfer = Channel.create()
 inferMetadata_assignedReads.splitCsv(sep: ",", header: false).separate(
-  assignedReads
+  assignedReadsInfer
 )
 
 /*