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/conf/multiqc_config.yaml

@@ -64,9 +64,9 @@ custom_data:
         pconfig:
             id: 'rid'
         headers:
-            'Replicate RID:'
-            'Experiment RID:'
-            'Study RID:'
+            Replicate RID
+            Experiment RID
+            Study RID
     meta:
         file_format: 'tsv'
         section_name: 'Metadata'
@@ -75,15 +75,15 @@ custom_data:
         pconfig:
             id: 'meta'
         headers:
-            'Source:'
-            'Species:'
-            'Ends:'
-            'Stranded:'
-            'Spike-in:'
-            'Raw Reads:'
-            'Assigned Reads:'
-            'Median Read Length:'
-            'Median TIN:'
+            Source
+            Species
+            Ends
+            Stranded
+            Spike-in
+            Raw-Reads
+            Assigned-Reads
+            Median-Length
+            Median-TIN
 
         file_format: 'tsv'
         section_name: 'TIN'