3.0.0

• Drop pre/post exec functions in mapping.sh
• Add ability to pair a groups file with fastq inputs to add info to readgroups
  in final BAM/CRAM files (PCAP-core).
• BWA 0.7.17 - bug fixes for future alpine building.
• Biobambam2 2.0.84 - via pre-compiled versions
• HTSlib + Samtools 1.7
• PCAP-core 4.1.1
  • mismatchQc options added
• cgpBigWig 1.0.0 (via dockstore-cgpbigwig 2.0.0)
• Examples moved to more useful naming, now have:
  • examples/bamOutput and examples/cramOutput each containing:
    • bam_input.json
    • fastq_gz_input.json - with yaml groupinfo file example.
• Multiple CWL descriptors one for BAM output, another for CRAM, legacy version retained.
  • Ensure you use the correct json examples.
• Now using secondaryFiles for outputs to reduce repetitive entries in cwl and json.
  • Bugfix to dockstore tool needed for output provisioning, 1.3.6+