2.4.0 Added run-cgprna command line tool and CWL workflows

• Reduced Docker image size
• Added run-cgprna command line tool, which can be used to complete a step in RNA-seq data workflow with just one command. Currently 4 subcommands are implemented:
  • map: uses star_mapping.pl to map and marks duplicates after mapping.
  • stats: generates mapping stats using bam_stats and RSeQC.
  • bigwig: generates bigwig file using bamToBw.pl
  • counts: counts reads using htseq-count.
• Built a new set of reference files for run-cgprna to use. They're available on ftp://ftp.sanger.ac.uk/pub/cancer/support-files/cgpRna_container/.
• CWL tools and workflows:
  • added a workflow to map sample by lanes, generate mapping stats for lanes, merge lane bams, generate bigwig file and count reads.
  • added CWL tools/workflows for the workflow above to use.
  • added example JSON for most of the CWL files.