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

@@ -1026,7 +1026,7 @@ process aggrQC {
 
     # remove inner distance report if it is empty (SE repRID)
     echo -e "LOG: removing dummy inner distance file" >> ${repRID}.aggrQC.log
-    if [ wc -l ${innerDistance} | awk '{print\${1}}' -eq 0 ]
+    if [ "${endsM}" == "se" ]
     then
       rm -f ${innerDistance}
     fi
@@ -1035,4 +1035,4 @@ process aggrQC {
     echo -e "LOG: running multiqc" >> ${repRID}.aggrQC.log
     multiqc -c ${multiqcConfig} . -n ${repRID}.multiqc.html
     """
-}
+}
\ No newline at end of file