Skip to content

ED add stub tests to subworkflows#820

Open
emmadizdarevic wants to merge 23 commits into
devfrom
ED-add-stub-tests
Open

ED add stub tests to subworkflows#820
emmadizdarevic wants to merge 23 commits into
devfrom
ED-add-stub-tests

Conversation

@emmadizdarevic
Copy link
Copy Markdown
Contributor

@emmadizdarevic emmadizdarevic commented Apr 22, 2026 •
edited
Loading

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/raredisease branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Ensure the test suite passes (nextflow run . -profile test_singleton,docker --outdir <OUTDIR>).
  • 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).

@nf-core-bot
Copy link
Copy Markdown
Member

nf-core-bot commented Apr 22, 2026

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.5.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

@emmadizdarevic
Copy link
Copy Markdown
Contributor Author

emmadizdarevic commented Apr 22, 2026

@nf-core-bot fix linting

@github-actions
Copy link
Copy Markdown

github-actions Bot commented Apr 22, 2026 •
edited
Loading

nf-core pipelines lint overall result: Failed ❌

Posted for pipeline commit e14a945

+| ✅ 243 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗   8 tests had warnings |!
-| ❌   1 tests failed       |-
Details

❌ Test failures:

  • merge_markers - Merge marker '<<<<<<<' in /home/runner/work/raredisease/raredisease/CHANGELOG.md: <<<<<<< HEAD

❗ Test warnings:

  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/raredisease/raredisease/subworkflows/local/align_sentieon/main.nf: _ mq_metrics = SENTIEON_DATAMETRICS.out.mq_metrics.ifEmpty(null) // channel: [ val(meta), path(mq_metrics) ]
    _
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/raredisease/raredisease/subworkflows/local/align_sentieon/main.nf: _ qd_metrics = SENTIEON_DATAMETRICS.out.qd_metrics.ifEmpty(null) // channel: [ val(meta), path(qd_metrics) ]
    _
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/raredisease/raredisease/subworkflows/local/align_sentieon/main.nf: _ gc_metrics = SENTIEON_DATAMETRICS.out.gc_metrics.ifEmpty(null) // channel: [ val(meta), path(gc_metrics) ]
    _
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/raredisease/raredisease/subworkflows/local/align_sentieon/main.nf: _ gc_summary = SENTIEON_DATAMETRICS.out.gc_summary.ifEmpty(null) // channel: [ val(meta), path(gc_summary) ]
    _
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/raredisease/raredisease/subworkflows/local/align_sentieon/main.nf: _ aln_metrics = SENTIEON_DATAMETRICS.out.aln_metrics.ifEmpty(null) // channel: [ val(meta), path(aln_metrics) ]
    _
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/raredisease/raredisease/subworkflows/local/align_sentieon/main.nf: _ is_metrics = SENTIEON_DATAMETRICS.out.is_metrics.ifEmpty(null) // channel: [ val(meta), path(is_metrics) ]
    _
  • schema_lint - Input mimetype is missing or empty
  • schema_description - No description provided in schema for parameter: hisat2

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-raredisease_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_dark.png
  • modules_config - modules_config

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.1
  • Run at 2026-04-29 12:33:12

@emmadizdarevic emmadizdarevic changed the title Ed add stub tests ED add stub tests to subworkflows Apr 22, 2026
@emmadizdarevic
Copy link
Copy Markdown
Contributor Author

emmadizdarevic commented Apr 28, 2026

@nf-core-bot fix linting

@emmadizdarevic emmadizdarevic marked this pull request as ready for review April 29, 2026 13:47
@emmadizdarevic
Copy link
Copy Markdown
Contributor Author

emmadizdarevic commented Apr 30, 2026

@nf-core-bot fix linting

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

No reviews

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

@emmadizdarevic @nf-core-bot