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@ODiogoSilva ODiogoSilva released this 21 Sep 20:13
· 204 commits to master since this release
1.3.0
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Learn about vigilant mode.

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
Assets 2