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Shinyngs/staticdifferential #2399

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merged 15 commits into from
Nov 7, 2022

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pinin4fjords
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@pinin4fjords pinin4fjords commented Oct 26, 2022

Just a simple module wrapper for https://github.com/pinin4fjords/shinyngs/blob/develop/exec/differential_plots.R, useful for making differential plots in differential analysis workflows. Right now it's just making volcano plots, but will be extended in future.

Notes;

  • I've tried to adhere to the feedback given for related PRs (see Shinyngs/app #2315, Shinyngs/staticexploratory #2364)
  • The matrix data provided in the second channel is not currently used in the command. But I believe it will be necessary for future differential plots that leverage expression data (rather than just differential statistics as volcano plots do), so I've added the input channel to facilitate that.

PR checklist

Closes #2398

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Emit the versions.yml file.
  • Follow the naming conventions.
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  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
    • PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
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@jfy133 jfy133 left a comment

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mostly LGTM but needs to remove the presumeed meta information from the module

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Jonathan Manning and others added 4 commits November 4, 2022 11:42
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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Once you've dropped the meta fields then LGTM

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Thanks @jfy133 for review, hopefully I fully addressed your points in that final commit. I'll also look into submitting the analogous fix on deseq2/differential.

@pinin4fjords pinin4fjords merged commit 36c30c9 into nf-core:master Nov 7, 2022
@pinin4fjords pinin4fjords deleted the shinyngs/staticdifferential branch November 7, 2022 12:01
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new module: shinyngs/static_differential
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