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Fix non-conformable arrays bug#221

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WackerO merged 13 commits intoqbic-pipelines:devfrom
WackerO:nonconf_fix
May 3, 2024
Merged

Fix non-conformable arrays bug#221
WackerO merged 13 commits intoqbic-pipelines:devfrom
WackerO:nonconf_fix

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@WackerO WackerO commented Oct 13, 2023 •
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This fixes the following error:

Quitting from lines 1083-1345 (RNAseq_report.Rmd) 
  Error in padj_bin * logFC_bin : non-conformable arrays
  Calls: <Anonymous> ... withVisible -> eval_with_user_handlers -> eval -> eval

which happens for some datasets. It also adds the padj value to the volcano plot hovertext (see section 5.2) and sets the dot colors to fixed values independently of whether DE genes are found or not:

Uploading RNAseq_report_nonconf.html.zip…

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 Oct 13, 2023 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit f5b1da2

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

❌ 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 06:17:17

d4straub
d4straub approved these changes May 2, 2024
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LGTM, again no comment, maybe I am not the right person for reviewing this pipeline since it was usually not (not yet?) applicable to my data...

@WackerO WackerO merged commit 545faee into qbic-pipelines:dev May 3, 2024
@WackerO WackerO deleted the nonconf_fix branch May 3, 2024 06:52
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@d4straub d4straub d4straub approved these changes

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@WackerO @d4straub
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