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

@@ -298,7 +298,7 @@ process trimData {
     hostname > ${repRID}.trimData.log
     ulimit -a >> ${repRID}.trimData.log
 
-    # trim fastq's using trim_galore
+    # trim fastq's using trim_galore and extract median read length
     echo -e "LOG: trimming ${ends}" >> ${repRID}.trimData.log
     if [ "${ends}" == "se" ]
     then
@@ -875,7 +875,8 @@ process countData {
       featureCounts -T `nproc` -a ./genome.gtf -G ./genome.fna -g 'gene_name' -o ${repRID}.countData -s \${stranding} -p -B -R SAM --primary --ignoreDup ${repRID}.sorted.deduped.bam
     fi
     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
@@ -887,6 +888,12 @@ process countData {
     """
 }
 
+// Extract number of assigned reads metadata into channel
+assignedReadsInfer = Channel.create()
+inferMetadata_assignedReads.splitCsv(sep: ",", header: false).separate(
+  assignedReads
+)
+
 /*
  *fastqc: run fastqc on untrimmed fastq's
 */
@@ -911,12 +918,6 @@ process fastqc {
     """
 }
 
-// Extract number of assigned reads metadata into channel
-assignedReadsInfer = Channel.create()
-inferMetadata_assignedReads.splitCsv(sep: ",", header: false).separate(
-  assignedReads
-)
-
 /*
  *dataQC: calculate transcript integrity numbers (TIN) and bin as well as calculate innerdistance of PE replicates
 */