Skip to content

feat: add configs for GPU optimizations#10

Open
amandazhuyilan wants to merge 2 commits intomainfrom
dev-gpu-optimized
Open

feat: add configs for GPU optimizations#10
amandazhuyilan wants to merge 2 commits intomainfrom
dev-gpu-optimized

Conversation

@amandazhuyilan
Copy link
Collaborator

@amandazhuyilan amandazhuyilan commented Feb 23, 2026

This draft pull request captures the configuration changes for optimizing bindflow for running on Kunbeternetes clusted powered GPU instances.

More details are captured in this document (please request access if needed).

@github-actions
Copy link

github-actions bot commented Feb 23, 2026 •
edited
Loading

nf-core pipelines lint overall result: Failed ❌

Posted for pipeline commit bf27d8c

+| ✅ 161 tests passed       |+
#| ❔  26 tests were ignored |#
!| ❗  26 tests had warnings |!
-| ❌   6 tests failed       |-
Details

❌ Test failures:

  • nextflow_config - Config default value incorrect: params.quote_char is set as " in nextflow_schema.json but is `` in nextflow.config.
  • nextflow_config - Default value from the Nextflow schema params.project = za08`` not found in nextflow.config.
  • nextflow_config - Default value from the Nextflow schema params.use_dgxa100 = False`` not found in nextflow.config.
  • schema_params - Param k8s_workdir from nextflow config not found in nextflow_schema.json
  • schema_params - Default value for param project invalid: Not in pipeline parameters. Check nextflow.config.
  • schema_params - Default value for param use_dgxa100 invalid: Not in pipeline parameters. Check nextflow.config.

❗ 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 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
  • 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 gadi_test.config: Specify the paths to your test data on nf-core/test-datasets
  • pipeline_todos - TODO string in gadi_test.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 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 test.config: Specify the paths to your test data on nf-core/test-datasets
  • pipeline_todos - TODO string in test.config: Give any required params for the test so that command line flags are not needed
  • 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 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 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.
  • schema_params - Schema param project not found from nextflow config
  • schema_params - Schema param use_dgxa100 not found from nextflow config

❔ Tests ignored:

  • files_exist - File is ignored: conf/igenomes.config
  • files_exist - File is ignored: conf/igenomes_ignored.config
  • files_exist - File is ignored: conf/igenomes.config
  • files_exist - File is ignored: conf/igenomes_ignored.config
  • files_exist - File is ignored: CODE_OF_CONDUCT.md
  • files_exist - File is ignored: assets/nf-core-bindflow_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-bindflow_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-bindflow_logo_dark.png
  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • nextflow_config - Config variable ignored: validation.help.beforeText
  • nextflow_config - Config variable ignored: validation.help.afterText
  • nextflow_config - Config variable ignored: validation.summary.beforeText
  • nextflow_config - Config variable ignored: validation.summary.afterText
  • files_unchanged - File ignored due to lint config: CODE_OF_CONDUCT.md
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
  • files_unchanged - File ignored due to lint config: assets/nf-core-bindflow_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-bindflow_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-bindflow_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/bindflow/bindflow/.github/workflows/awstest.yml

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2026-02-25 05:06:32

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.

1 participant

@amandazhuyilan