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

@@ -877,10 +877,7 @@ process countData {
     echo -e "LOG: counted" >> ${repRID}.countData.log
     
     # extract assigned reads
-    assignedReads=\$(grep -m 1 'Assigned' *.countData.summary | grep -oe '\\([0-9.]*\\)')
-    echo -e \${assignedReads} > assignedReads.csv
-    echo -e "LOG: assigned reads: "\${assignedReads} >> ${repRID}.countData.log
-
+    grep -m 1 'Assigned' *.countData.summary | grep -oe '\\([0-9.]*\\)') > assignedReads.csv
 
     # calculate TPM from the resulting countData table
     echo -e "LOG: calculating TPM with R" >> ${repRID}.countData.log