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.

Sign up for GitHub

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

Jump to bottom

scGPT cell classification workflow #786

Closed
wants to merge 161 commits into from
Closed

scGPT cell classification workflow #786

wants to merge 161 commits into from

Conversation

jakubmajercik
Copy link
Collaborator

@jakubmajercik jakubmajercik commented Apr 14, 2024 •
edited by dorien-er
Loading

Changelog

Implementation of workflow for cell type classification with scGPT

Issue ticket number and link

Closes #777

Checklist before requesting a review

  • I have performed a self-review of my code

  • Conforms to the Contributor's guide

  • Check the correct box. Does this PR contain:

    • Breaking changes
    • New functionality
    • Major changes
    • Minor changes
    • Documentation
    • Bug fixes

  • Proposed changes are described in the CHANGELOG.md

  • CI tests succeed!

dorien-er and others added 30 commits March 6, 2024 11:16
@dorien-er
preproc script
78954c0
@dorien-er
preproc script
9068e7a
@dorien-er
tokenize and pad script
dbe5204
@dorien-er
tokenize and pad script
89a9c6a
@dorien-er
embedding script
9e446f8
@dorien-er
test resourcers and evaluation script
94dd10c
@dorien-er
cross check gene set
3edf3c0
@dorien-er
pad_tokenize module
085cdc4
@dorien-er
updat image
724427e
@dorien-er
remove test resources, update inputs
f9aadfa
@dorien-er
use pytorch image
33c9ffe
@dorien-er
remove integration component
0c6316d
@dorien-er
remove nvidia reqs
47f5dda
@jakubmajercik
Merge branch 'main' of github.com:openpipelines-bio/openpipeline into…
9d2ffd0 
… scgpt
@dorien-er
remove load_model option
0f74ebd
@jakubmajercik
base script and config added
7b4f39c
@DriesSchaumont @dorien-er
Fix retag for viash-hub not using correct namespace separator (#745)
52fb38c
@DriesSchaumont @dorien-er
CI - Build: Fix second occurance of namespace separator (#746)
accf980
@jakubmajercik
config extended + logger set up + tests in progress
fdf310e
@jakubmajercik
Merge branch 'scgpt-dev' of github.com:openpipelines-bio/openpipeline…
dfffe11 
… into 747-generate-scgpt-cross_check_genes-module
@dorien-er
script to download scgpt test data
b1dd6ce
@dorien-er
remove test resources script
18db6d6
@dorien-er
adjust preprocessing script
6c3fec0
@dorien-er
add scgpt full preproc module
acd3600
@dorien-er
integration submodule
3e31204
@dorien-er
integration submodule and add normalize_total flag
b5d1970
@dorien-er
add params
ec326f8
@dorien-er
Merge pull request #751 from openpipelines-bio/scgpt-preprocessor
2dddc1c 
scGPT integration preproc module
@dorien-er @DriesSchaumont
Add script to download scgpt test resources (#750)
dbb0ea5 
* add script to download scgpt test resources

* Update resources_test_scripts/scgpt.sh

Co-authored-by: Dries Schaumont <[email protected]>

* add drive folders containing data and model

* chmod +x

---------

Co-authored-by: Dries Schaumont <[email protected]>
@dorien-er
embedding module
adcd6f0
dorien-er and others added 21 commits April 24, 2024 17:08
@dorien-er
fix typo
0ae8cdb
@dorien-er
Merge pull request #761 from openpipelines-bio/embed
a5977ea 
scGPT embedding component
@jakubmajercik @dorien-er @DriesSchaumont
Generate scgpt cross check genes module (#758)
638ac50 
* base script and config added

* config extended + logger set up + tests in progress

* config working + script improved + tests in progress

* exception handling, extended tests

* extended tests + better logging

* changelog entry added

* test resource path in config fixed

* python test setup added to config

* PR comments fixed

* updated to use subset data

* remove batch id column logic

* update authors

* resources, tests and dependencies fixes

* update key name input output

* update key name input output

* update var gene names

* update config

* compression param added + minor fixes

---------

Co-authored-by: dorien-er <[email protected]>
Co-authored-by: DriesSchaumont <[email protected]>
@dorien-er
Merge branch 'scgpt' into 777-implement-scgpt-cell-type-annotation-wo…
fc511c1 
…rkflow
@dorien-er
rebase
a14862b
@dorien-er
temporary workaround test
296bff1
@dorien-er
update workflow without new state output
de8b34f
@dorien-er
retry workflow_output
7bc9afc
@dorien-er
fetch workflow output from state
78f6eed
@dorien-er
remove temporary workflow workaround
9dc65e5
@dorien-er
update name and namespace
7ddc66f
@dorien-er
remove outdated component
bf16216
@dorien-er
update
63ffdcf
@dorien-er
update config
8c7bd69
@dorien-er
update params
6ab2906
@dorien-er
update cell_type script and params
914f8b8
@dorien-er
update integration test
b598221
@dorien-er
fix dependency resolutions
eb0d5dc
@dorien-er
resolve config path
c534af9
@dorien-er
fix typo
e7b70ba
@dorien-er
fix integration test
8e5880f
dorien-er
dorien-er previously approved these changes May 9, 2024
View reviewed changes
@dorien-er dorien-er changed the title 777 implement scgpt cell type annotation workflow scGPT cell classification workflow May 9, 2024
Base automatically changed from scgpt to main June 14, 2024 13:42
@DriesSchaumont DriesSchaumont dismissed dorien-er’s stale review June 14, 2024 13:42

The base branch was changed.

@dorien-er dorien-er closed this Jul 8, 2024
@jakubmajercik jakubmajercik linked an issue Jul 8, 2024 that may be closed by this pull request
implement scGPT cell type annotation workflow #777
Open
@dorien-er
Copy link
Contributor

This functionality has moved taken up in branch 'annotation-workflow'

@dorien-er dorien-er deleted the 777-implement-scgpt-cell-type-annotation-workflow branch July 8, 2024 13:07
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@dorien-er dorien-er dorien-er left review comments

@DriesSchaumont DriesSchaumont Awaiting requested review from DriesSchaumont

Assignees

@jakubmajercik jakubmajercik

Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

implement scGPT cell type annotation workflow
5 participants
@jakubmajercik @dorien-er @DriesSchaumont @VladimirShitov @KaiWaldrant