Skip to content

SampleSheet Parsing API endpoint #962

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

Open
alexiswl opened this issue Apr 15, 2025 · 1 comment
Open

SampleSheet Parsing API endpoint #962

alexiswl opened this issue Apr 15, 2025 · 1 comment
Assignees
Labels
feature New feature

Comments

@alexiswl
Copy link
Member

alexiswl commented Apr 15, 2025

Realising that we now have:

Would rather pull these into one repository.

If extracting pandas from the former is too difficult then I propse a microservice for this instead (or propose an API as an option anyway and a good use-case for a new service on the new org).

Where one can:

  1. Parse samplesheets from Json to CSV and vice versa
  2. Validate a samplesheet, given a samplesheet and a mocked up RunInfo.xml file, run a validation which then runs bclconvert --validate-samplesheet-only.

There are a few scenarios that could find this useful.

  1. The samplesheet checker that needs to return a v2 samplesheet
  2. The samplesheet checker that should valdiate a v2 samplesheet with bclconvert --validate-samplesheet-only
  3. The sequence run manager that stores the samplesheet in JSON format.
  4. ctTSOv2 service that needs to make a samplesheet in order to run the workflow
@alexiswl alexiswl added the feature New feature label Apr 15, 2025
@raylrui
Copy link
Contributor

raylrui commented Apr 16, 2025

Pull these into one repository seems great.
Currently 'v2-samplesheet-parser' is also use the Section Classes from 'v2-samplesheet-maker'. We can keep these settings and tools consistency after combination.

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

No branches or pull requests

2 participants