142 convert faqcs output pdf into interactive html#144
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Pull Request Overview
This PR implements generation of a new interactive QC_final_report.html and integrates QA stats into the existing workflow.
- Renames and refines QC stats emissions to separate text and matrix outputs, and adds a new QA stats emit.
- Introduces QC_final_report.html output and updates the
jsonQCstatsprocess to consume both text and QA stats. - Adds a
--debugflag to the QC process for increased verbosity.
Comments suppressed due to low confidence (1)
workflows/Nextflow/modules/runFaQCs/runFaQCs.nf:85
- [nitpick] Including
--debugin the production QC process may generate excessive log output and slow down execution. Consider making this flag configurable or removing it for regular runs.
--debug \
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aw-watson
approved these changes
Jul 17, 2025
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This pull request is the implementation to generate QC_final_report.html file.
@yxu-lanl please help with the integration into output page:
The QC_summary_plots.html can be used in the result page.
The QC_final_report.html has more plot which can be a [report] link on the top of the iframe for user want to see more figures.
If the long reads has been used as input, there is NanoPlot-report.html which should be used as [report] link instead.