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Allow flexibility in meta map usage with Deseq2 #2476

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merged 7 commits into from
Nov 8, 2022

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@pinin4fjords pinin4fjords commented Nov 7, 2022

PR checklist

This PR establishes some consistency with feedback from @jfy133 in another PR. Essentially we should not be 'baking in' assumptions about the content meta maps, but rather allowing the workflow-level usage to pass that.

So, where the R template was previously reading the meta directly, it now receives the meta options like by setting the following in the workflow configs:

ext.args = { "--contrast_variable $meta.variable --reference_level $meta.reference --treatment_level $meta.target --blocking_variables $meta.blocking "}

I've also tweaked the bare-bones option parsing there to allow for blank values passed that way.

  • 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.
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  • Add a resource label
  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • 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
    • PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware

@pinin4fjords pinin4fjords changed the title Deseq no meta assumptions Allow flexibility in meta map usage with Deseq2 Nov 7, 2022
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Other than those two comments, LGTM!

modules/nf-core/deseq2/differential/templates/deseq_de.R Outdated Show resolved Hide resolved
modules/nf-core/deseq2/differential/templates/deseq_de.R Outdated Show resolved Hide resolved
Jonathan Manning and others added 3 commits November 8, 2022 09:03
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Thanks for the review @WackerO

@pinin4fjords pinin4fjords merged commit 46e4580 into nf-core:master Nov 8, 2022
@pinin4fjords pinin4fjords deleted the deseq_no_meta_assumptions branch November 8, 2022 09:53
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2 participants