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/splitStudy.py

+#!/usr/bin/env python3
+
+import argparse
+import pandas as pd
+import warnings
+warnings.simplefilter(action='ignore', category=FutureWarning)
+
+def get_args():
+    parser = argparse.ArgumentParser()
+    parser.add_argument('-s', '--studyRID',help="The study RID.",required=True)
+    args = parser.parse_args()
+    return args
+
+def main():
+    args = get_args()
+    studyRID=pd.read_json(args.studyRID+"_studyRID.json")
+    if studyRID["RID"].count() > 0:
+        studyRID["RID"].to_csv(args.studyRID+"_studyRID.csv",header=False,index=False)
+    else:
+        raise Exception("No associated replicates found: %s" %
+            studyRID)
+
+if __name__ == '__main__':
+    main()