Report!!

Introducing the new Report system that is hosted by the Flowcraft web application. With the new report mode, it is now possible to visualize the reports of a flowcraft pipeline in the browser, either at the end of the pipeline run or in real-time while the pipeline is in execution.

Features

• Added report run mode to Flowcraft that displays the report of any given
  pipeline in the Flowcraft's web application. The report mode can be executed
  after a pipeline ended or during the pipeline execution using the --watch
  option.
• Added standalone report HTML at the end of the pipeline execution.
• Components with support for the new report system:
  • abricate
  • assembly_mapping
  • check_coverage
  • chewbbaca
  • dengue_typing
  • fastqc
  • fastqc_trimmomatic
  • integrity_coverage
  • mlst
  • patho_typing
  • pilon
  • process_mapping
  • process_newick
  • process_skesa
  • process_spades
  • process_viral_assembly
  • seq_typing
  • trimmomatic
  • true_coverage

Minor/Other changes

• Refactored report json for components mash_dist, mash_screen and
  mapping_patlas

Bug fixes

• Fixed issue where seq_typing and patho_typing processes were not feeding
  report data to report compiler.
• Fixed fail messages for process_assembly and process_viral_assembly
  components