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Merged
scwatts merged 3 commits into from
Dec 3, 2025
Merged

Update tests and relevant GH Actions workflows / actions #265

scwatts merged 3 commits into from
Dec 3, 2025

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@scwatts scwatts commented Nov 20, 2025 •
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  • added real full size data to the test_full profile
    • HCC1395 (SEQC-II) tumour / normal WGS with tumour WTS
  • enabled test profile in GH Actions
    • the data in this profile requires more than 32 GB memory and ~200 GB disk space to complete analysis
    • staying with default RunOns runners the most suitable choice for the workload is 32cpu-linux-x64
    • however this runner is considerably overprovisioned for smaller (and more standard) tests
    • the nf-test GH Action was refactored and generalised to accommodate different test sizes
    • splitting tests avoids needlessly wasting compute resources on overprovisioned large runners
    • please see this successful GH Action run of the refactored workflow for reference
  • update test snapshots

@scwatts
Split CICD nf-test tests into small and large
f655de0 
In order to run the 'test' profile on nf-core CICD, a large RunsOn
instance is required with more 32 GB memory. We will eventually have
many small tests but don't want these to also wastefully run on large
instances. To avoid this situation, I split tests into different sizes
where only the larger tests run on the up-sized instance.
@scwatts
Add full sized data to full test profile
a3aa015
@scwatts scwatts requested a review from rhassaine November 20, 2025 04:16
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nf-core-bot commented Nov 20, 2025

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.4.1.
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.

@scwatts scwatts mentioned this pull request Nov 20, 2025
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github-actions bot commented Nov 20, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit d423215

+| ✅ 208 tests passed       |+
#| ❔  12 tests were ignored |#
!| ❗  15 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • files_unchanged - LICENSE does not match the template
  • 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!
  • schema_params - Schema param panel not found from nextflow config
  • schema_params - Schema param fastp_umi_location not found from nextflow config
  • schema_params - Schema param fastp_umi_length not found from nextflow config
  • schema_params - Schema param fastp_umi_skip not found from nextflow config
  • schema_params - Schema param redux_umi_duplex_delim not found from nextflow config
  • schema_params - Schema param genome_version not found from nextflow config
  • schema_params - Schema param genome_type not found from nextflow config
  • schema_params - Schema param ref_data_hmf_data_path not found from nextflow config
  • schema_params - Schema param ref_data_panel_data_path not found from nextflow config
  • schema_params - Schema param ref_data_genome_gtf not found from nextflow config
  • schema_description - No description provided in schema for parameter: prepare_reference_only

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.1
  • Run at 2025-12-03 05:39:48

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scwatts commented Nov 20, 2025

Force pushing clean history containing fixes for linter

@scwatts scwatts mentioned this pull request Nov 28, 2025
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scwatts commented Dec 3, 2025

Force pushing again with additional changes, cleaned commits

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scwatts commented Dec 3, 2025 •
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@rayanhassaine adding an alternative reviewer as discussed

@scwatts scwatts changed the title Update input data for 'test_full' profile, and enable 'test' profile in GH Actions Update tests and relevant GH Actions workflows / actions Dec 3, 2025
@scwatts scwatts requested a review from luan-n-nguyen December 3, 2025 05:19
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scwatts commented Dec 3, 2025

Force pushing with commits rebased on top of latest dev

@scwatts scwatts merged commit 25c37d6 into dev Dec 3, 2025
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@scwatts scwatts deleted the update-tests branch December 3, 2025 23:02
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@luan-n-nguyen luan-n-nguyen luan-n-nguyen approved these changes

@rhassaine rhassaine rhassaine approved these changes

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@scwatts @nf-core-bot @luan-n-nguyen @rhassaine