Skip to content

Add annotate_cadd subworkflow test#794

Draft
peterpru wants to merge 1 commit into
devfrom
add-annotate-cadd-subworkflow-tests
Draft

Add annotate_cadd subworkflow test#794
peterpru wants to merge 1 commit into
devfrom
add-annotate-cadd-subworkflow-tests

Conversation

@peterpru
Copy link
Copy Markdown
Member

@peterpru peterpru commented Mar 24, 2026

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).

@peterpru peterpru self-assigned this Mar 24, 2026
@nf-core-bot
Copy link
Copy Markdown
Member

nf-core-bot commented Mar 24, 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.

@github-actions
Copy link
Copy Markdown

github-actions Bot commented Mar 24, 2026 •
edited
Loading

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 84b9da0

+| ✅ 234 tests passed       |+
#| ❔   7 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗   8 tests had warnings |!
Details

❗ 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 fixed:

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.1
  • Run at 2026-03-24 18:35:56

@peterpru peterpru mentioned this pull request Mar 25, 2026
Open
34 tasks
@kristinebilgrav kristinebilgrav mentioned this pull request Mar 30, 2026
Merged
kristinebilgrav added a commit to Clinical-Genomics/oncorefiner that referenced this pull request Apr 23, 2026
@kristinebilgrav
feat: Add cadd for indels (#59)
7422634 
Closes
Clinical-Genomics/MTP-oncoflow#27

### Added

- CADD score annotation for indels
    - created a subworkflow for the process (annotate_cadd)
        - Only runs if the val_cadd_resources is populated 
    - added modules GAWK, CADD and TABIX
- compatibility with both GRCh37 and GRCh38 (although only tested with
proper data and resources for GRCh38 - see issue for more details)
- test for subworkflow: 
- NOTE: cadd resources are very large, which makes creating a test
dataset hard, but this is being worked on in raredisease
nf-core/raredisease#794. We can update the test
when this is completed. Therefore:
        - the subworkflow test is run in `stub` mode only currently    
        - the default test does not run the annotate_cadd subworkflow 

#### Test on hasta
 - The test for GRCh38 was successful (see issue for more details)
 - The test for GRCh37 was not run due to lack of resources.
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

No reviews

Assignees

@peterpru peterpru

Labels

None yet

Projects

None yet

Milestone

No milestone

Development

Successfully merging this pull request may close these issues.

2 participants

@peterpru @nf-core-bot