Skip to content

Pseudo PR against TEMPLATE for checking the pipeline #33

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
Draft
wants to merge 322 commits into
base: TEMPLATE
Choose a base branch
from
Draft

Pseudo PR against TEMPLATE for checking the pipeline #33

wants to merge 322 commits into from

Conversation

JudithBernett
Copy link
Collaborator

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/drugresponseeval 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>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

PascalIversen and others added 30 commits August 1, 2024 17:00
@PascalIversen @JudithBernett
test mode not needed
3af2b0b
@PascalIversen @JudithBernett
black
7382c8b
@JudithBernett
Merge branch 'main' of github.com:JudithBernett/nf-core-drugresponseeval
a466aa9
@PascalIversen @JudithBernett
Revert "todos for @pascal #8"
b8e62be 
This reverts commit d69219c.
@JudithBernett
Merge branch 'main' of github.com:JudithBernett/nf-core-drugresponseeval
498c4e4
@JudithBernett
redundancy removed, closes #8
c1e78a0
@JudithBernett
Cross-study prediction is now supported, closes #2. Also some visuali…
9c21936 
…zation fixes
@JudithBernett
Critical difference plot included and drawn successfully
73ab053
@JudithBernett
Added docker and singluarity containers to config - testing wave, mig…
ad72844 
…ht switch back though
@JudithBernett
3 cpus allowed for training
fde1769
@JudithBernett
Update README.md
149d057
@JudithBernett
trying to restructure everything such that SingleDrugModels can be tr…
50d17f4 
…ained in parallel
@PascalIversen
fix make model channel
9e0d1ec
@PascalIversen
fixing commas
d788b66
@PascalIversen
.
a0e1eed
@PascalIversen
improves eval code
74773de
@JudithBernett
Merge branch 'main' of github.com:JudithBernett/nf-core-drugresponseeval
f1e03ca
@JudithBernett
pipeline runs for elasticnet + toydata
5837dde
@JudithBernett
fixed cross study
bcb8fce
@JudithBernett
I think it's fixed for singledrugmodels?
5d20b30
@JudithBernett
updated readme
36c462e
@JudithBernett
Merge branch 'main' into single_model_restructuring
e496f39
@JudithBernett
trying to consolidate results - does not work yet
637918e
@JudithBernett
consolidating results! Now works for --models SingleDrugRandomForest …
f95a292 
…--baselines NaivePredictor with randomization and robustness test.
@JudithBernett
pipeline also works for cross validation now
417bac2
@JudithBernett
fixed that hyperparameter split is just executed per model class, not…
09d7b71 
… model instance
@JudithBernett
fixed error in consolidate_results.py
b4d8185
@JudithBernett
had limited cpus to 3
6f3d58a
@JudithBernett
trying to have gpu support
71467ba
@JudithBernett
trying to have gpu support pt. 2: only for specific models
8669fd3
JudithBernett and others added 30 commits June 5, 2025 17:22
@JudithBernett
Merge remote-tracking branch 'origin/dev' into nf-core-template-merge…
675774f 
…-3.3.1
@JudithBernett
Merge branch 'dev' of github.com:nf-core/drugresponseeval into dev
4df298c
@JudithBernett
added authors and licenses to python scripts: closes #40. Moved publi…
2e4b61d 
…shDir directives to modules.config: closes #41.
@JudithBernett
updated CHANGELOG.md
b0ca819
@JudithBernett
Merge branch 'dev' into nf-core-template-merge-3.3.1
402999b
@JudithBernett
new day, new try!
a4f6486
@JudithBernett
I have this file now, just without mqc
cf8bd69
@JudithBernett
snap outdated - should work now? :))))
3379a56
@mashehu
template bug fix
b76aab6
@JudithBernett
Merge branch 'nf-core-template-merge-3.3.1' of github.com:nf-core/dru…
6283013 
…gresponseeval into nf-core-template-merge-3.3.1
@JudithBernett
trying the hacky solution
18180ce
@JudithBernett
Merge pull request #39 from nf-core/nf-core-template-merge-3.3.1
a4cba10 
Important! Template update for nf-core/tools v3.3.1
@JudithBernett
Merge branch 'dev' of github.com:nf-core/drugresponseeval into dev
9592a9e
@JudithBernett
Merge pull request #42 from nf-core/add_license_change_publishdir
9da18e5 
Add license change publishdir
@JudithBernett
Merge branch 'dev' of github.com:nf-core/drugresponseeval into dev
66e65a9
@JudithBernett
updated the drevalpy version, bumped docker to python 3.13, added unz…
13e8b5a 
…ip to the docker
@JudithBernett
local env files because nf-test doesn't like it
f0f6954
@JudithBernett
removed hacky torch solution, replaced it with nice solution
d8b8dfc
@JudithBernett
added ProteomicsElasticNet, SingleDrugProteomicsRandomForest support
a28625b
@JudithBernett
added no_hyperparameter_tuning flag for quick runs/debugging
c9ac09b
@JudithBernett
added dataset_name to DrugResponseDataset.from_csv, making tissue col…
1dc8785 
…umn optional
@JudithBernett
added the possibility to train a final model
2b382bf
@JudithBernett
missed new readme content for ro-crate-metadata.json
bc700c3
@JudithBernett
parallelized the hyperparameter tuning for the final model
2aaf38b
@JudithBernett
added output and usage information
5e46315
@JudithBernett
this does not need resources
e83aeda
@JudithBernett
forgot response transformation on training final model
782798e
@JudithBernett
drevalpy v 1.3.4
430b13c
@JudithBernett
removed PR TEMPLATE changes
668a60c
@JudithBernett
Merge pull request #43 from nf-core/update_1_3_3
00ebfdd 
Update to drevalpy v1.3.4
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
5 participants
@JudithBernett @nf-core-bot @PascalIversen @picciama @mashehu