Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Workflow Execution: Sample Name Cell Component #678

Merged
merged 4 commits into from
Aug 6, 2024

Conversation

ksierks
Copy link
Contributor

@ksierks ksierks commented Jul 30, 2024

What does this PR do and why?

Updated the SamplesheetComponent to include sample names.
See http://localhost:3000/rails/lookbook/inspect/nextflow_samplesheet/default.
Fixes #670.

Screenshots or screen recordings

Screenshot from 2024-07-30 13-47-40

How to set up and validate locally

  1. Add add-sample-name to versions within the pipelines.json file. (Reference https://github.com/phac-nml/iridanextexample/tree/add-sample-name)
  2. Run sapporo-service.
  3. Run irida-next.
  4. Execute the newly added pipeline add-sample-name.
  5. Verify the sample name is displayed within the sample sheet.

PR acceptance checklist

This checklist encourages us to confirm any changes have been analyzed to reduce risks in quality, performance, reliability, security, and maintainability.

@ksierks ksierks self-assigned this Jul 30, 2024
@ksierks ksierks force-pushed the sample-name-cell-component branch from b9883a5 to 1c0c55b Compare July 30, 2024 17:44
@ksierks
Copy link
Contributor Author

ksierks commented Jul 31, 2024

On hold as pipelines failing on validation with sample names that contain spaces.

@ksierks ksierks force-pushed the sample-name-cell-component branch 2 times, most recently from 2470078 to 4bb67ed Compare August 2, 2024 16:27
@ksierks ksierks removed the on hold label Aug 6, 2024
@ksierks ksierks marked this pull request as ready for review August 6, 2024 15:57
Copy link
Member

@ericenns ericenns left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Just a minor comment, otherwise this looks good.

test/fixtures/files/nextflow/schema_input.json Outdated Show resolved Hide resolved
test/fixtures/files/nextflow/samplesheet_schema.json Outdated Show resolved Hide resolved
@ksierks ksierks force-pushed the sample-name-cell-component branch from c5da1c6 to 8143748 Compare August 6, 2024 16:08
Copy link
Member

@ericenns ericenns left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Looks good to me!

Copy link

github-actions bot commented Aug 6, 2024

Simplecov Report

Covered Threshold
92.67% 90%

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

Workflow Execution: Sample Name Cell Component
2 participants