Resolve "process_count"

Add featureCounts (including manual TPM calculation in R: decided not to calculate FPKM because they are essentially the same thing, and since Data-Hub requested TPM, that's what was calulated)

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!
• Replace dag.png with the most recent CI pipleine integrated_pe artifact

• Close issue
  Closes #56 (closed)

/cc @ghenry @venkat.malladi

workflow/scripts/calculateTPM.R

+gc()
+library(optparse)
+
+option_list=list(
+  make_option("--count",action="store",type='character',help="Count File")
+)
+opt=parse_args(OptionParser(option_list=option_list))
+rm(option_list)
+
+if (!("count" %in% names(opt))){
+  stop("No count file passed, exiting.")
+} else if (!file.exists(opt$count)) {
+  stop("No count file passed, exiting.")
+}
+
+repRID <- basename(gsub(".featureCounts","",opt$count))
+
+count <- read.delim(opt$count, comment.char="#") # if featureCounts file changes structure, be sure to update count and Length columns below
+colnames(count)[7] <- "count"
+
+rpk <- count$count/count$Length/1000
+
+scale <- sum(rpk)/1000000
+
+tpm <- rpk/scale
+
+output <- cbind(count,tpm)
+colnames(output)[7] <- "count"
+
+write.table(output,file=paste0(repRID,".countTable.csv"),sep=",",row.names=FALSE,quote=FALSE)