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Migrate Summarizedexperiment module from rnaseq workflow #4890

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merged 13 commits into from
Feb 13, 2024

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pinin4fjords
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@pinin4fjords pinin4fjords commented Feb 9, 2024

Also fix tx2gene so its tables have column headers and deal with fallout of that.

Will need a merge of the test data nf-core/test-datasets#1093

PR checklist

  • 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.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • 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 requested a review from a team as a code owner February 9, 2024 14:12
@pinin4fjords pinin4fjords requested review from vagkaratzas and removed request for a team February 9, 2024 14:12
@pinin4fjords pinin4fjords changed the title Migrate Summarizedexperiment modules from rnaseq workflow Migrate Summarizedexperiment module from rnaseq workflow Feb 9, 2024
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Thanks @maxulysse !

@pinin4fjords pinin4fjords added this pull request to the merge queue Feb 13, 2024
Merged via the queue into master with commit 105968d Feb 13, 2024
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@pinin4fjords pinin4fjords deleted the summarizedexperiment branch February 13, 2024 10:38
jch-13 pushed a commit to jch-13/modules that referenced this pull request Mar 19, 2024
* tx2gene should add column names

* Finalise summarized experiment

* tx2gene should put column names on its output

* tx2gene has column ids now

* Temporarily repoint test data

* Fix linting issues

* Try to appease eclint

* finish appeasing ecling

* Remove rogue g from tidying up line endings

* Remove rogue g from tidying up line endings

* Update test_data.config
jennylsmith pushed a commit to RSC-RP/modules that referenced this pull request Mar 20, 2024
* tx2gene should add column names

* Finalise summarized experiment

* tx2gene should put column names on its output

* tx2gene has column ids now

* Temporarily repoint test data

* Fix linting issues

* Try to appease eclint

* finish appeasing ecling

* Remove rogue g from tidying up line endings

* Remove rogue g from tidying up line endings

* Update test_data.config
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2 participants