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Cellenics integration

Open kafkasl opened this issue 3 years ago • 2 comments

Issue being solved: https://github.com/nf-core/scrnaseq/issues/156

PR checklist

  • [ ] This comment contains a description of changes (with reason).
  • [ ] If you've fixed a bug or added code that should be tested, add tests!
  • [ ] If you've added a new tool - have you followed the pipeline conventions in the contribution docs- [ ] If necessary, also make a PR on the nf-core/scrnaseq branch on the nf-core/test-datasets repository.
  • [ ] Make sure your code lints (nf-core lint).
  • [ ] Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
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  • [ ] README.md is updated (including new tool citations and authors/contributors).

kafkasl avatar Oct 11 '22 08:10 kafkasl

This PR is against the master branch :x:

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @kafkasl,

It looks like this pull-request is has been made against the biomage-org/scrnaseq master branch. The master branch on nf-core repositories should always contain code from the latest release. Because of this, PRs to master are only allowed if they come from the biomage-org/scrnaseq dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page. Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

github-actions[bot] avatar Oct 11 '22 08:10 github-actions[bot]

nf-core lint overall result: Passed :white_check_mark:

Posted for pipeline commit 423b4c3

+| ✅ 158 tests passed       |+

:white_check_mark: Tests passed:

Run details

  • nf-core/tools version 2.6
  • Run at 2022-11-18 08:53:40

github-actions[bot] avatar Oct 11 '22 08:10 github-actions[bot]

I think that this PR requires a higher level discussion on whether and/or how commercial services should be integrated. Who maintains these parts? Which commercial products would qualify and which ones not? Don't think that this conversation converged in https://github.com/nf-core/scrnaseq/issues/156

Zethson avatar Nov 22 '22 15:11 Zethson

Thank you for bringing this up @Zethson. I can understand caution with commercial services.

Cellenics is not a commercial service. It's an open source project out of Harvard Medical School. It can be, and has been, independently deployed using the open source code and open source deployment scripts hosted by Harvard here: https://github.com/hms-dbmi-cellenics

It's true that many people working on Cellenics work at BioMage (including me), and it's true that a lot of deployments of Cellenics these days are installed by BioMage for commercial customers. But the product itself is fully open source (and fully and independently functional as an open source project).

One of the important decisions of keeping this integration interoperable with independent deployments of Cellenics is allowing the user to specify the URL of Cellenics instance that they want to send the data to (the plugin is not limited to e.g. community instance hosted by BioMage).

We (BioMage) will maintain parts responsible for the integration.

picrin avatar Nov 22 '22 18:11 picrin

I'm closing this now as this kind of functionality should now be handled via nextflow plugins, which are now mature. Having various "upload to XXX" modules at the end of the pipeline creates an unreasonable maintenance burden.

grst avatar Mar 07 '24 11:03 grst