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/scripts/tinHist.py

@@ -35,7 +35,9 @@ def main():
     hist = hist.T.fillna(0.0).astype(int)
     #hist = hist.apply(lambda x: x/x.sum()*100, axis=1)
     hist.to_csv(args.repRID + '.tin.hist.tsv',sep='\t')
-    tin['TIN'][(tin['TIN']!=0)].median().to_csv(args.repRID + '.tin.med.csv',sep=',')
+    medFile = open(args.repRID + '.tin.med.csv',"w")
+    medFile.write(str(round(tin['TIN'][(tin['TIN']!=0)].median())))
+    medFile.close()
 
 if __name__ == '__main__':
-    main()
\ No newline at end of file
+    main()