nf-core/drugresponseeval
Pipeline for testing drug response prediction models in a statistically and biologically sound way.
Define the models and baselines to be tested.
Model to be tested.
stringNaiveDrugMeanPredictorBaselines to be tested.
stringNaiveMeanEffectsPredictorDefine where the pipeline should find input data and save output data.
Run name for the pipeline. The subdirectory in results will be named like this.
stringmy_runName of the dataset. Pre-supplied datasets are CTRPv2, CTRPv1, CCLE, GDSC1, GDSC2, TOYv1, TOYv2.
stringCTRPv2The output directory where the results will be saved. Default is results/
stringresultsEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Define the mode in which the pipeline will be run.
Run the pipeline in test mode LPO (Leave-random-Pairs-Out), LCO (Leave-Cell-line-Out), or LDO (Leave-Drug-Out).
stringLCOOptions for randomization.
Randomization mode for the pipeline.
stringNoneRandomization type for the pipeline.
stringOptions for robustness.
Number of trials to run for the robustness test
integerOptions for data input.
Path to the data directory.
stringdataThe name of the drug response measure to use.
stringDatasets for cross-study prediction.
stringLink to the latest Zenodo version of the dataset.
stringhttps://zenodo.org/records/15533857/files/^https://zenodo.org/records/[0-9]+/files/$Additional options for the pipeline.
False by default (=refitting). By default, we use measures calculated with CurveCurator instead of original measures reported by the authors for the available datasets, or invoke automatic fitting of custom raw viability data with CurveCurator. Set this flag to disable this option.
booleanOptimization metric for the pipeline.
stringNumber of cross-validation splits.
integer10Response transformation
stringModel checkpoint directory
stringTEMPORARYDisable hyperparameter tuning.
booleanTrain final model on full data.
booleanParameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringLess common options for the pipeline, typically set in a config file.
Display version and exit.
booleanMethod used to save pipeline results to output directory.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Send plain-text email instead of HTML.
booleanDo not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringBoolean whether to validate parameters against the schema at runtime
booleantrueBase URL or local path to location of pipeline test dataset files
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.
string