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).