Cleanup output of TB Sample Report pipeline

COMBAT-TB / irida-pipeline-plugins

Galaxy pipelines as plugin for IRIDA intergration

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Cleanup output of TB Sample Report pipeline #9

Closed pvanheus closed 3 years ago

pvanheus commented 3 years ago

The current pipeline output shows outputs from zipped HTML that are unreadable and JSON that has little visual value.

The IRIDA code hides zip, html and pdf output previews but the output name of the HTML outputs are mtbva_tb_variant_report_html and mtbva_tb_variant_dr_report_html. These names should be changed in the output workflow to ensure that they are not displayed.

The JSON output is named tb_profiler_json and should also be renamed to .json for easier filtering on the IRIDA end.

pvanheus commented 3 years ago

Current output has been cleaned up a bit "too much":

What is needed in addition to what is shown there is:

TB VCF text report
TB VCF HTML report (downloadable - because this is a zip file)
SnpEff annotated VCF

The last item in the list is in addition to TBprofiler VCF.

zipho commented 3 years ago

Please verify as the plugin is updated