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First release!#22

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PascalIversen merged 122 commits intomainnf-core/drugresponseeval:mainfrom devnf-core/drugresponseeval:devCopy head branch name to clipboardJan 31, 2025

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Commits on Oct 4, 2024

• consolidating results! Now works for --models SingleDrugRandomForest --baselines NaivePredictor with randomization and robustness test.

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Commits on Oct 8, 2024

• pipeline also works for cross validation now

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• Template update for nf-core/tools version 3.0.0

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Commits on Oct 9, 2024

• Template update for nf-core/tools version 3.0.1

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Commits on Oct 11, 2024

• Template update for nf-core/tools version 3.0.2

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Commits on Oct 28, 2024

• fixed that hyperparameter split is just executed per model class, not model instance

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• fixed error in consolidate_results.py

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• had limited cpus to 3

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Commits on Oct 31, 2024

• trying to have gpu support

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• trying to have gpu support pt. 2: only for specific models

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• doesn't work yet - setting label to process_gpu everywhere for now

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• doesn't work yet - setting label to process_gpu everywhere for now

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• forgot the brackets

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Commits on Nov 4, 2024

• copying results

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• more cpus for train_and_predict

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Commits on Nov 15, 2024

• incorporated updates from the package

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• Merge branch 'dev' into nf-core-template-merge-3.0.1

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• fixed pre-commit

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• Merge branch 'nf-core-template-merge-3.0.1' into single_model_restructuring

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• Merge pull request #10 from nf-core/nf-core-template-merge-3.0.1

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• Merge branch 'dev' of github.com:nf-core/drugresponseeval into dev

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• removed fastqc, multiqc. Removed max_multiqc_email_size from schema. Added input=null for linting in the nextflow.config

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• changed gitignore to include intellij .idea folder

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• fixed linting

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• fixed pre-commit

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• trying to get the new logos

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• new logos

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• new logos

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• Merge branch 'TEMPLATE' of github.com:nf-core/drugresponseeval into TEMPLATE

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• going to document more

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• trying to fix the images

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• trying to fix images #2

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• trying to fix logo part 3

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• Found the problem. The hack is to switch to the TEMPLATE branch and copy the logo files from there and move them over.

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• trying to fix .nf-core.yml check

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• it didn't update?

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Commits on Nov 18, 2024

• fixed -profile test but still need to put the requirements on docker and the dataset on nf-core/test-datasets

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Commits on Nov 21, 2024

• added container with latest drevalpy version

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Commits on Nov 22, 2024

• added conda support

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• Proper usage documentation

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• Proper output documentation, removed unnecessary statements in the module files

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• change log for the pull request

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• added citations for implemented and adapted drug response prediction models

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Commits on Nov 25, 2024

• trying to fix version comment

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• trying to fix ci.yml

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• trying to fix ci.yml

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• rolling back ci.yml

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• does this template_version_comment.yml update now?

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• Remove unnecessary statements in .nf-core.yml

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• remove unnecessary statements in .nf-core.yml

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• Merge branch 'linting_and_testing' of github.com:nf-core/drugresponseeval into linting_and_testing

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• sorted the cited implemented tools alphabetically, renamed the pipeline picture and added more alt-text

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• ignoring input parameter

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• forgot to remove input from nextflow.config

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• Merge pull request #11 from nf-core/linting_and_testing

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• intermediate commit, added CurveCurator logic

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• Merge branch 'dev' into feature/curvecurator_module

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Commits on Nov 26, 2024

• Merge branch 'dev' of github.com:nf-core/drugresponseeval into dev

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Commits on Nov 29, 2024

• does not work with path_data as path, need it as val for -resume to work

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Commits on Dec 2, 2024

• adjusted params for new drevalpy handling

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• ensured output and task requirements are correct

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Commits on Dec 3, 2024

• fixed missing measure arg and fit_curves includes

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• syntax error fix in call to FIT_CURVES

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• fix missing comma in call to RUN_CV

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• added default measure and fixed arg type

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• add missing path_data arg to params_check

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• fix syntax errors and wrong args / file modes

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• fixed argument parsing bug

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• add missing dataset_name arg

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Commits on Dec 4, 2024

• separated fitting into three modules

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• fixed paths and emits

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• fixed publishDirs

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• fixed missing params ref in publishDir

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• ensure LOAD_RESPONSE is waiting

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Commits on Dec 5, 2024

• fixed path data problems, problem was missing params. in front of path_data in publishDir.

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• created separate preprocessing workflow

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• added missing commas

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• Merge branch 'feature/curvecurator_module' of https://github.com/picciama/drugresponseeval into feature/curvecurator_module

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• giving path_data as value, not as channel, does not work otherwise

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• giving back valid measure variables:

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Commits on Dec 10, 2024

• remove trailing whitespaces

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Commits on Dec 12, 2024

• Template update for nf-core/tools version 3.1.0

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Commits on Dec 16, 2024

• c

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• checkpointing

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Commits on Dec 20, 2024

• Template update for nf-core/tools version 3.1.1

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Commits on Jan 13, 2025

• deleted notes

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• Merge branch 'feature/curvecurator_module' of https://github.com/picciama/drugresponseeval into feature/curvecurator_module

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• changing something small to retrigger github action

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• schema

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• pre-commit

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• auto fix lint nfcore

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• Merge branch 'dev' into nf-core-template-merge-3.1.1

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• Merge branch 'nf-core-template-merge-3.1.1' of github.com:nf-core/drugresponseeval into nf-core-template-merge-3.1.1

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• fixed pre-commit

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• fixed container and env to latest

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• Merge branch 'nf-core-template-merge-3.1.1' into global_checkpoint_dir

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• Merge pull request #16 from nf-core/global_checkpoint_dir

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• Merge branch 'dev' of https://github.com/picciama/drugresponseeval into dev

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• merged latest dev version

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• Merge branch 'dev' of github.com:nf-core/drugresponseeval into dev

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• Merge branch 'dev' into fix/datapath

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• ./data -> data

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Commits on Jan 20, 2025

• Template update for nf-core/tools version 3.1.2

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Commits on Jan 27, 2025

• Template update for nf-core/tools version 3.2.0

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Commits on Jan 29, 2025

• Lots of fixes:

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• did not work with relative default path yet, maybe now

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• updated documentation

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• Merge pull request #18 from nf-core/fix/datapath

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• Merge branch 'dev' of https://github.com/picciama/drugresponseeval into dev

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• merged latest dev version

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• Merge branch 'dev' into nf-core-template-merge-3.2.0

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• Merge pull request #20 from nf-core/nf-core-template-merge-3.2.0

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• fixed schema

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• Merge branch 'dev' of https://github.com/picciama/drugresponseeval into dev

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• Merge branch 'dev' into feature/curvecurator_module

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Commits on Jan 30, 2025

• fixed curvecurator-related tasks to work within the Nextflow logic, i.e., with the local paths in the work directories.

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• updated CITATIONS.md for curvecurator

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• updated CHANGELOG.md

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• minor changes

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• Merge pull request #14 from picciama/feature/curvecurator_module

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• Update env.yml

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• Merge pull request #21 from nf-core/JudithBernett-patch-1

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