Skip to content

Fix observation table column width for columns with NA#739

Open
grst wants to merge 2 commits into
devfrom
patch-report-na-variable
Open

Fix observation table column width for columns with NA#739
grst wants to merge 2 commits into
devfrom
patch-report-na-variable

Conversation

@grst
Copy link
Copy Markdown
Member

@grst grst commented May 29, 2026 •
edited
Loading

This fixes an error "! Can't coerce from -Inf to an integer." in case of columns with NAs.

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/differentialabundance branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nf-test test main.nf.test -profile test,docker).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,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).

@grst
Fix observation table column width for columns with NA
0255cfd 
This fixes an error "! Can't coerce from `-Inf` to an integer." in case
of columns with NAs.
@github-actions
Copy link
Copy Markdown

github-actions Bot commented May 29, 2026 •
edited
Loading

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 64c6fb7

+| ✅ 410 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗  12 tests had warnings |!
Details

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 2.0.0
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in nextflow.config: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in CONTRIBUTING.md: Add any pipeline specific contribution guidelines here, such as coding styles, procedures, checklists etc.
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • schema_lint - Parameter input is not defined in the correct subschema (input_output_options)
  • schema_description - No description provided in schema for parameter: dream_p_value
  • schema_description - No description provided in schema for parameter: dream_lfc

❔ Tests ignored:

  • files_exist - File is ignored: assets/multiqc_config.yml
  • nextflow_config - Config default ignored: params.report_file
  • nextflow_config - Config default ignored: params.logo_file
  • nextflow_config - Config default ignored: params.css_file
  • nextflow_config - Config default ignored: params.citations_file
  • files_unchanged - File ignored due to lint config: assets/nf-core-differentialabundance_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-differentialabundance_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-differentialabundance_logo_dark.png
  • multiqc_config - multiqc_config

✅ Tests passed:

Run details

  • nf-core/tools version 4.0.2
  • Run at 2026-05-29 06:52:26

@grst grst requested a review from pinin4fjords May 29, 2026 06:51
@grst grst mentioned this pull request May 29, 2026
Open
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

@atrigila atrigila atrigila approved these changes

@pinin4fjords pinin4fjords Awaiting requested review from pinin4fjords

Assignees

No one assigned

Labels

None yet

Projects

None yet

Milestone

No milestone

Development

Successfully merging this pull request may close these issues.

2 participants

@grst @atrigila