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Gostplot fix, comp methods change#212

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WackerO merged 3 commits intoqbic-pipelines:devfrom
WackerO:dev
Jul 31, 2023
Merged

Gostplot fix, comp methods change#212
WackerO merged 3 commits intoqbic-pipelines:devfrom
WackerO:dev

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@WackerO WackerO commented Jul 28, 2023 •
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The layout of the gostplots was previously not working, the interactive moving did not function. This PR fixes that problem. It also adds a computational methods section to the report even if no software_versions were provided

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 Jul 28, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 084a987

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

❗ 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 2023-07-28 15:31:51

@WackerO
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WackerO commented Jul 28, 2023

Reminder: Push changelog!

SusiJo
SusiJo approved these changes Jul 28, 2023
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LGTM!

@WackerO WackerO merged commit f2183ea into qbic-pipelines:dev Jul 31, 2023
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@SusiJo SusiJo SusiJo approved these changes

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