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ci: update runner storage, lint workflow, and repository assets - #66

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BilalsGituation merged 2 commits into
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ci/test-80gb-volume
Oct 29, 2026
Merged

ci: update runner storage, lint workflow, and repository assets#66
BilalsGituation merged 2 commits into
devfrom
ci/test-80gb-volume

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@vmduarut

@vmduarut vmduarut commented Oct 29, 2026 •
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Summary

  • Configure an 80 GB RunsOn runner volume for nf-test jobs in .github/workflows/nf-test.yml.
  • Update the lint workflow: use nf-core/setup-nextflow@v3, select Python 3.15, and change the pinned astral-sh/setup-uv action to v10.3.2; also update the actions/setup-python version comment.
  • Clean up obsolete and broad .gitignore entries while retaining the specific nf-test directory and log entries.
  • Refresh the light logo in assets/ and the dark logo in docs/images/.

Status and scope

  • Per the reported status: The runner volume issue is resolved. Remaining linting failures should be addressed separately in a follow-up PR.

Validation

  • Workflow YAML and runner labels were checked locally.
  • CI validation is pending; nf-test and nf-core lint jobs are still running or queued.

@github-actions

github-actions Bot commented Oct 29, 2026 •
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nf-core pipelines lint overall result: Failed ❌

Posted for pipeline commit 6cff9e5

+| ✅ 229 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗  41 tests had warnings |!
-| ❌   2 tests failed       |-
Details

❌ Test failures:

  • files_unchanged - assets/nf-core-pathogenepidemiology_logo_light.png does not match the template
  • files_unchanged - docs/images/nf-core-pathogenepidemiology_logo_dark.png does not match the template

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in CHANGELOG.md: ## v0.1.0dev - [unreleased replace with date on release ]
  • pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
  • pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
  • pipeline_todos - TODO string in README.md: TODO nf-core:
  • pipeline_todos - TODO string in README.md: Include a figure that guides the user through the major workflow steps. Many nf-core
  • pipeline_todos - TODO string in README.md: Fill in short bullet-pointed list of the default steps in the pipeline 1. Read QC (FastQC)2. Present QC for raw reads (MultiQC)
  • pipeline_todos - TODO string in README.md: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
  • pipeline_todos - TODO string in README.md: update the following command to include all required parameters for a minimal example
  • pipeline_todos - TODO string in README.md: If applicable, make list of people who have also contributed
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file
  • 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
  • pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
  • pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
  • 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 test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • 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 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 meta.yml: # Add a description of the module and list keywords
  • pipeline_todos - TODO string in meta.yml: #Add a description and other details for the software below
  • pipeline_todos - TODO string in meta.yml: ##Add a description of all of the variables used as input
  • pipeline_todos - TODO string in meta.yml: ##Add a description of all of the variables used as output
  • pipeline_todos - TODO string in environment.yml: List required Conda package(s).
  • pipeline_todos - TODO string in main.nf: Optional inputs are not currently supported by Nextflow. However, using an empty
  • pipeline_todos - TODO string in main.nf: A stub section should mimic the execution of the original module as best as possible
  • pipeline_todos - TODO string in main.nf: If the module doesn't use arguments ($args), you SHOULD remove:
  • pipeline_todos - TODO string in main.nf.test: Once you have added the required tests, please run the following command to build this file:
  • pipeline_todos - TODO string in main.nf.test: Change the test name preferably indicating the test-data and file-format used
  • pipeline_todos - TODO string in main.nf.test: If you are created a test for a chained module
  • pipeline_todos - TODO string in main.nf.test: define inputs of the process here. Example:
  • pipeline_todos - TODO string in main.nf.test: //Add all required assertions to verify the test output.
  • pipeline_todos - TODO string in main.nf.test: Change the test name preferably indicating the test-data and file-format used but keep the " - stub" suffix.
  • pipeline_todos - TODO string in main.nf.test: define inputs of the process here. Example:
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here

❔ Tests ignored:

  • 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

✅ Tests passed:

Run details

  • nf-core/tools version 4.2.1
  • Run at 2026-10-29 15:40:58

@github-actions

github-actions Bot commented Oct 29, 2026 •
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❌ nf-test failed with latest Nextflow version

Note

Tests with Nextflow's latest version failed but it will not cause a CI workflow failure.
Please check if the failure is expected with newer (edge-)releases of Nextflow or if it needs fixing.

  • ❌ docker | latest-everything | Shard 1/7

See the full run for details.

@vmduarut vmduarut changed the title ci: test nf-test runners with an 80 GB volume ci: update runner storage, lint workflow, and repository assets Oct 29, 2026
@BilalsGituation
BilalsGituation merged commit b9dde7c into dev Oct 29, 2026
17 of 21 checks passed
@BilalsGituation
BilalsGituation deleted the ci/test-80gb-volume branch October 29, 2026 15:46
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@BilalsGituation BilalsGituation Awaiting requested review from BilalsGituation
@igiraclement igiraclement Awaiting requested review from igiraclement

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@vmduarut @BilalsGituation