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theiagen / public_health_bioinformatics

Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health concern.
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[feature request] add new output columns for Freyja QC values #287

Closed kapsakcj closed 6 months ago

kapsakcj commented 8 months ago

:cool:

:pushpin: Explain the Request

A user requested that the Freyja QC values (such as coverage) are outputted to the Terra data table instead of being only available in the output file.

:books: Context

Requested by DE lab (so far)

:chart_with_upwards_trend: Desired Behavior

Add necessary output column(s) to Freyja workflow

:information_source: Additional Information

will edit this Issue with more info as I learn more

emmadoughty commented 7 months ago

Plan:

  1. Identify Freyja QC outputs to add. @kapsakcj Please let me know if you have any more information about PHL interests
  2. Amend task_freyja_one-sample.wdl command block to capture values from the output file in the data table; add to the outputs section of the task file
  3. Identify test data
  4. Test?
  5. Amend wf_freyja_fastq.wdl to add new QC outputs in the wf outputs section
  6. Test!