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Update RNAseq_report.Rmd #228

Merged
merged 2 commits into from
May 3, 2024
Merged

Update RNAseq_report.Rmd #228

merged 2 commits into from
May 3, 2024

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qbicStefanC
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Update RNAseq_report.Rmd for DE information

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
  • 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).

@qbicStefanC
Update RNAseq_report.Rmd
114ecfa 
Update RNAseq_report.Rmd for DE information
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This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @qbicStefanC,

It looks like this pull-request is has been made against the qbic-pipelines/rnadeseq master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the qbic-pipelines/rnadeseq dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

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github-actions bot commented Mar 26, 2024 •
edited
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nf-core lint overall result: Failed ❌

Posted for pipeline commit dbefe1b

+| ✅ 145 tests passed       |+
#| ❔  26 tests were ignored |#
!| ❗   8 tests had warnings |!
-| ❌  14 tests failed       |-

❌ Test failures:

  • files_exist - File must be removed: lib/Utils.groovy
  • files_exist - File must be removed: lib/WorkflowMain.groovy
  • files_exist - File must be removed: lib/NfcoreTemplate.groovy
  • files_exist - File must be removed: lib/WorkflowRnadeseq.groovy
  • files_exist - File must be removed: lib/nfcore_external_java_deps.jar
  • nextflow_config - Config default value incorrect: params.software_versions is set as None in nextflow_schema.json but is NO_FILE6 in nextflow.config.
  • nextflow_config - Config default value incorrect: params.genome is set as None in nextflow_schema.json but is null in nextflow.config.
  • nextflow_config - Config default value incorrect: params.publish_dir_mode is set as copy in nextflow_schema.json but is null in nextflow.config.
  • nextflow_config - Config default value incorrect: params.email is set as false in nextflow_schema.json but is null in nextflow.config.
  • nextflow_config - Config default value incorrect: params.custom_config_base is set as https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version} in nextflow_schema.json but is https://raw.githubusercontent.com/nf-core/configs/master in nextflow.config.
  • nextflow_config - Config default value incorrect: params.config_profile_description is set as false in nextflow_schema.json but is null in nextflow.config.
  • nextflow_config - Config default value incorrect: params.config_profile_contact is set as false in nextflow_schema.json but is null in nextflow.config.
  • nextflow_config - Config default value incorrect: params.config_profile_url is set as false in nextflow_schema.json but is null in nextflow.config.
  • files_unchanged - .github/workflows/linting_comment.yml does not match the template

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.
  • 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 awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • pipeline_todos - TODO string in rnadeseq.nf: Add all file path parameters for the pipeline to the list below
  • 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
  • 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 2.13.1
  • Run at 2024-05-03 06:58:10

@qbicStefanC qbicStefanC changed the base branch from master to dev March 26, 2024 09:49
@qbicStefanC qbicStefanC requested a review from WackerO March 26, 2024 09:50
WackerO
WackerO approved these changes Mar 27, 2024
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Good catch!

@WackerO WackerO merged commit 6313e20 into dev May 3, 2024
17 of 18 checks passed
@WackerO WackerO deleted the qbicStefanC-patch-1 branch May 3, 2024 10:53
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@WackerO WackerO WackerO approved these changes

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@qbicStefanC @WackerO