Release 5.0.0

• Update default CPAT version to 3.0.4.
• Use gffcompare to merge stringtie assembly GTF files, rather than stringtie merge.
• Add call to create annotation file for shiny app.
• Add call to create design matrix template for shiny app.
• Add predex v0.9.2 container to dockerImages.
• dockerImages.yml: update umitools (v1.1.1) image with correct version of samtools (1.10).
• test/cromwell_options.json: add memory attribute.
• dockerImages.yml: update umitools to version 1.1.1 (multi-package including samtools).
• Replace travis with github CI.
• Add the dockerImages to the output section.
• Make running stringtie optional by exposing the boolean
  runStringtieQuantification.
• Downgrade stringtie to version 1.3.6, as version 2 returns unstranded
  transcripts which is incompatible with htseq-count.
• When multiple TPM/FPKM values are returned for a single gene by
  stringtie, they will now be added together in the multi-sample
  expression tables. Previously only the last value encountered would be
  used.
• Updated default docker image for collect-columns (now uses version 1.0.0
  instead of 0.2.0).