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Added boxplots after batcheffect; boxplots now from transformed data; boxplot titles and filenames now also with genename; increased threshold before overlapping PCA labels are hidden #215

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merged 6 commits into from
Aug 17, 2023
Merged

Added boxplots after batcheffect; boxplots now from transformed data; boxplot titles and filenames now also with genename; increased threshold before overlapping PCA labels are hidden #215

merged 6 commits into from
Aug 17, 2023

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WackerO
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@WackerO WackerO commented Aug 15, 2023 •
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Boxplots are now generated not from raw, but from transformed counts. If batcheffect, will plot them before and after transformation. The plot titles and filenames now also contain their genenames in addition to the geneIDs. Also, in the PCA label plots, the threshold for hiding overlapping labels has been increased

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/rnadeseq 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 Aug 15, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 4957b14

+| ✅ 126 tests passed       |+
#| ❔  26 tests were ignored |#
!| ❗   8 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in rnadeseq.nf: Add all file path parameters for the pipeline to the list below
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • schema_lint - Parameter input is not defined in the correct subschema (input_output_options)

❔ Tests ignored:

  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: assets/multiqc_config.yaml
  • files_exist - File is ignored: assets/nf-core-qbic-pipelines/rnadeseq_logo_light.png
  • files_exist - File is ignored: bin/markdown_to_html.r
  • files_exist - File is ignored: conf/test_full.config
  • files_exist - File is ignored: docs/images/nf-core-qbic-pipelines/rnadeseq_logo_dark.png
  • files_exist - File is ignored: docs/images/nf-core-qbic-pipelines/rnadeseq_logo_light.png
  • files_exist - File is ignored: lib/WorkflowQbic-pipelines/rnadeseq.groovy
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • nextflow_config - Config variable ignored: params.input
  • files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/config.yml
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/feature_request.yml
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • 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: assets/sendmail_template.txt
  • files_unchanged - File ignored due to lint config: docs/README.md
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-08-17 09:58:22

@WackerO
added logical to the boxplots after batcheffect; removed quotes from …
fd4e336 
…the gene_list table that is written to metadata
@WackerO WackerO changed the title Added boxplots after batcheffect; boxplots now from transformed data Added boxplots after batcheffect; boxplots now from transformed data; boxplot titles and filenames now also with genename Aug 16, 2023
@WackerO WackerO changed the title Added boxplots after batcheffect; boxplots now from transformed data; boxplot titles and filenames now also with genename Added boxplots after batcheffect; boxplots now from transformed data; boxplot titles and filenames now also with genename; increased threshold before overlapping PCA labels are hidden Aug 17, 2023
@WackerO WackerO merged commit ff84b38 into qbic-pipelines:dev Aug 17, 2023
18 checks passed
@WackerO WackerO deleted the boxplots branch August 17, 2023 11:44
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@mirpedrol mirpedrol mirpedrol approved these changes

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@WackerO @mirpedrol