theiagen / public_health_bioinformatics

Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health concern.
GNU General Public License v3.0
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Add FastQC & FastP reports as TheiaProk outputs #336

Closed emily-smith1 closed 6 months ago

emily-smith1 commented 8 months ago

:pushpin: Explain the Request

Adding reports generated by FastQC & FastP as outputs to the TheiaProk_Illumina_PE_PHB workflow. Both tools are already run within the workflow, but the reports aren't output, just individual metrics.

:books: Context

Additional visuals with per-base QC metrics. Eventual ingestion into MultiQC.

:chart_with_upwards_trend: Desired Behavior

Output columns containing reports from FastQC & FastP.

:information_source: Additional Information