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Implementation of nf-gpt into crisprseq pipeline. #193

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Implementation of nf-gpt into crisprseq pipeline. #193

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LeonHornich
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@LeonHornich LeonHornich commented Sep 2, 2024 •
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This is a very early stage implementation of the nf-gpt plugin into the pipeline. It can currently handles a list of genes extracted from the drugZ, bagel2 or mle module output and parses it to the plugin.

You can run the changes using:
export OPENAI_API_KEY=your-api-key
nextflow run . -profile test_screening,docker --outdir test -dump-channels --gpt_interpretation drugz,mle,bagel2,rra -resume

DISCLAIMER! You will need a functioning Open AI api key. for this to work.

Since this is very early version and only comes with the bare minimum of functionality there are a lot of adjustment that have to me made:

  • add option to generate multiple different responses per model and query.

Keep in mind this implementation does not aim to achieve 100% correct results from the gpt model, but instead is to build a foundational implementation for (future) LLMs into a nf-core pipeline.

If you have any suggestions or requested changes please let me know and i will try to adjust the code.

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github-actions bot commented Sep 2, 2024

This PR is against the master branch ❌

  • 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 @LeonHornich,

It looks like this pull-request is has been made against the LeonHornich/crisprseq 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 LeonHornich/crisprseq 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!

@LaurenceKuhl LaurenceKuhl changed the base branch from master to dev September 2, 2024 11:38
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github-actions bot commented Sep 2, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 05c4d56

+| ✅ 235 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   5 tests had warnings |!
-| ❌   1 tests failed       |-

❌ Test failures:

  • actions_ci - Minimum pipeline NF version '23.04.0' is not tested in '.github/workflows/ci.yml'

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 2.3.0
  • 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!

❔ Tests ignored:

  • files_exist - File is ignored: conf/test.config
  • files_exist - File is ignored: conf/test_full.config
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-09-19 11:53:17

Leon Hornich and others added 10 commits September 2, 2024 15:43
mirpedrol
mirpedrol reviewed Sep 12, 2024
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LaurenceKuhl
LaurenceKuhl reviewed Nov 11, 2024
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@LeonHornich @mirpedrol @LaurenceKuhl