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

@@ -910,8 +910,7 @@ process fastqc {
 
     # run fastqc
     echo -e "LOG: running fastq on raw fastqs" >> ${repRID}.fastqc.log
-    #fastqc *.fastq.gz -o .
-    touch test_fastqc.zip
+    fastqc *.fastq.gz -o .
     """
 }
 
@@ -1021,7 +1020,7 @@ process aggrQC {
     echo -e "LOG: creating metadata table" >> ${repRID}.aggrQC.log
     echo -e "Source\tSpecies\tEnds\tStranded\tSpike-in\tAssigned Reads\tRead Length\tTIN" > metadata.tsv
     echo -e "Infered\t${speciesI}\t${endsI}\t${strandedI}\t${spikeI}\t-\t-\t-" >> metadata.tsv
-    echo -e "Submitter\t${speciesM}\t${endsM}\t${strandedM}\t${spikeM}\t${readLengthM}\t-\t-" >> metadata.tsv
+    echo -e "Submitter\t${speciesM}\t${endsM}\t${strandedM}\t${spikeM}\t-\t${readLengthM}\t-" >> metadata.tsv
     echo -e "Measured\t-\t${endsManual}\t-\t-\t${assignedReadsI}\t${readLengthI}\t${tinMedI}" >> metadata.tsv
 
     # remove inner distance report if it is empty (SE repRID)