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DRAGEN: new module vc_hethom_ratio_metrics #1915

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@Just-Roma Just-Roma commented Apr 25, 2023

  • This comment contains a description of changes (with reason)

  • CHANGELOG.md has been updated

  • There is example tool output for tools in the https://github.com/ewels/MultiQC_TestData repository or attached to this PR

  • Code is tested and works locally (including with --lint flag)

  • docs/README.md is updated with link to below

  • docs/modulename.md is created

  • Everything that can be represented with a plot instead of a table is a plot
    Only linegraphs are included by default. Bargraphs can be also quickly included by setting BARGRAPHS_ENABLED
    to True. The variable is in the vc_hethom_ratio_metrics.py file.

  • Report sections have a description and help text (with self.add_section)

  • Module does not do any significant computational work

This module can be considered experimental: it can work in 2 modes by setting the variable SQUASH_SECTIONS in vc_hethom_ratio_metrics.py to True/False.

  1. If True, then only 1 section will be shown. Other sections can be chosen from a drop-list.
    This approach looks better but is unreliable, because hiding plots can break them when resizing/reloading html
    page. This bug seems to be common, at least the dragen_fastqc has the same issues.
  2. If False, then all sections are shown. The mentioned bugs are absent, but html report looks worse.

Merging:

  • merging this PR would require updates in dragen/dragen.py and multiqc/utils/search_patterns.yaml
    in PR1911, PR1912, PR1913, PR1914. But not in the dragen/utils.py, because it is the same. The main file must be also included, of course.

add search regex for .vc_hethom_ratio_metrics.csv files
Add hethom caller
Add common utils
@Just-Roma Just-Roma force-pushed the DRAGEN-New-Module-Hethom-Metrics branch from e7b0486 to 096cb63 Compare April 25, 2023 12:42
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