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New Pangolin module #1458

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merged 20 commits into from Jun 24, 2021
Merged

New Pangolin module #1458

merged 20 commits into from Jun 24, 2021

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ErikDanielsson
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@ErikDanielsson ErikDanielsson commented Jun 18, 2021

Wrote new module Pangolin module, according to specification given in #1454. It might be that there are too many columns in the generated table, since I didn't know what was essential and non-essential to the report.

  • 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
  • Report sections have a description and help text (with self.add_section)
  • There aren't any huge tables with > 6 columns (explain reasoning if so)
  • Each table column has a different colour scale to its neighbour, which relates to the data (eg. if high numbers are bad, they're red)
  • Module does not do any significant computational work

@ErikDanielsson ErikDanielsson changed the title Pangolin New Pangolin module Jun 18, 2021
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def parse_pangolin_log(self, fh):
contents = csv.DictReader(fh["f"])
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This is in a core Python library? I don't think I've ever used this before 🤯

Learn something new every day! 😆

@ErikDanielsson
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Thanks for all the tips! I'll have to look through all the changes you've made and give the docs a more thorough read.

@ewels ewels force-pushed the master branch 2 times, most recently from 3e19e54 to 9f00c19 Compare June 24, 2021 15:11
@ewels ewels merged commit 0285b60 into MultiQC:master Jun 24, 2021
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2 participants