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Add control features params for spike handling, and pass to updated DESeq2 module #18

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merged 4 commits into from
Nov 24, 2022
Merged

Add control features params for spike handling, and pass to updated DESeq2 module #18

merged 4 commits into from
Nov 24, 2022

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pinin4fjords
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@pinin4fjords pinin4fjords commented Nov 23, 2022 •
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This PR does the following in resolution of #12:

  • Bumps the DESeq module to incorporate Deseq2 spike handling modules#2534
  • Adds params for the control feature list and the boolean specifying whether controls should be used to derive scale factors
  • Passes the control features to the DESeq2 module.

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 pipeline conventions in the contribution docs- [ ] If necessary, also make a PR on the nf-core/differentialabundance branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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github-actions bot commented Nov 23, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 7c0b2b9

+| ✅ 154 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗  11 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in README.md: Add full-sized test dataset and amend the paragraph below if applicable
  • pipeline_todos - TODO string in README.md: If applicable, make list of people who have also contributed
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
  • pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.6
  • Run at 2022-11-23 11:38:29

@pinin4fjords pinin4fjords linked an issue Nov 23, 2022 that may be closed by this pull request
Handle spike sequences correctly #12
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@pinin4fjords pinin4fjords added the enhancement New feature or request label Nov 23, 2022
WackerO
WackerO approved these changes Nov 24, 2022
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LGTM

@pinin4fjords
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Thanks @WackerO !

@pinin4fjords pinin4fjords merged commit 19b5725 into nf-core:dev Nov 24, 2022
@pinin4fjords pinin4fjords deleted the spike_handling branch November 24, 2022 10:14
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@WackerO WackerO WackerO approved these changes

@ggabernet ggabernet Awaiting requested review from ggabernet

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Handle spike sequences correctly
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@pinin4fjords @WackerO