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Heatmap error, datasources, shorten filenames #225

Merged
merged 17 commits into from
Mar 5, 2024
Merged

Heatmap error, datasources, shorten filenames #225

merged 17 commits into from
Mar 5, 2024

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WackerO
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@WackerO WackerO commented Feb 20, 2024 •
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This PR fixes an error in the heatmaps, adds a parameter for the pathway analysis datasources and shortens some output file names

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).

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github-actions bot commented Feb 20, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 69855ac

+| ✅ 143 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 rnadeseq.nf: Add all file path parameters for the pipeline to the list below
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • 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 preferred methods description, e.g. add publication citation for this pipeline
  • 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.
  • 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
  • Run at 2024-02-29 10:13:38

@jonoave jonoave self-assigned this Feb 20, 2024
jonoave
jonoave approved these changes Feb 20, 2024
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@jonoave jonoave left a comment

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I think it should be fine.. :)

@WackerO WackerO changed the base branch from dev to master February 20, 2024 11:40
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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 @WackerO,

It looks like this pull-request is has been made against the WackerO/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 WackerO/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!

@WackerO WackerO changed the base branch from master to dev February 20, 2024 12:24
@WackerO WackerO merged commit 139b7e3 into qbic-pipelines:dev Mar 5, 2024
17 of 18 checks passed
@WackerO WackerO deleted the graphics branch March 5, 2024 12:35
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@WackerO @jonoave