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Change FILTER_DIFFTABLE to python because AWK does not correctly filter reliably#264

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WackerO merged 8 commits intonf-core:devfrom
WackerO:fix_filter_difftable
Apr 24, 2024
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Change FILTER_DIFFTABLE to python because AWK does not correctly filter reliably#264
WackerO merged 8 commits intonf-core:devfrom
WackerO:fix_filter_difftable

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@WackerO WackerO commented Apr 23, 2024 •
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This PR changes the FILTER_DIFFTABLE module to python with pandas; I noticed while working on #257 that the previous module sometimes filters out all the genes, not just the non-DE ones. I was not able to find where the issue is with AWK after a lot of trying out, so the module now uses python.
The module now also applies log2 to the threshold parameter so that the DE gene results are the same as in the report tables; I checked this and the tables now agree with each other (see attached zip).

filtered_results.zip

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github-actions bot commented Apr 23, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit d6f50cb

+| ✅ 268 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   5 tests had warnings |!
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❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 1.5.0
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-04-24 09:47:58

pinin4fjords
pinin4fjords requested changes Apr 23, 2024
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pinin4fjords approved these changes Apr 24, 2024
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Just a typo (and maybe make the actual PR name match what's in the changelog), otherwise good.

@WackerO WackerO changed the title Fix filter difftable Change FILTER_DIFFTABLE to python because AWK does not correctly filter reliably Apr 24, 2024
@WackerO WackerO merged commit c2d7ed0 into nf-core:dev Apr 24, 2024
@WackerO WackerO deleted the fix_filter_difftable branch April 24, 2024 11:26
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