nf-core/drugresponseeval
Pipeline for testing drug response prediction models in a statistically and biologically sound way.
1.0.0). The latest
stable release is
1.1.0
.
Define the models and baselines to be tested.
Model to be tested.
stringBaselines to be tested.
stringDefine where the pipeline should find input data and save output data.
Run ID for the pipeline.
stringName of the dataset.
stringThe output directory where the results will be saved. Default is results/
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Define the mode in which the pipeline will be run.
Run the pipeline in test mode LPO (Leave-random-Pairs-Out), LCO (Leave-Cell-line-Out), or LDO (Leave-Drug-Out).
stringLPOOptions for randomization.
Randomization mode for the pipeline.
stringRandomization type for the pipeline.
stringpermutationOptions for robustness.
Number of trials to run for the robustness test
integerOptions for data input.
Path to the data directory.
stringThe name of the measure to use
stringLN_IC50Datasets for cross-study prediction.
stringAdditional options for the pipeline.
If True, use refit measures instead of original measures reported by the authors for the available datasets, or invoke automatic fitting of custom raw viability data.
booleanOptimization metric for the pipeline.
stringRMSENumber of cross-validation splits.
integer10Response transformation
stringModel checkpoint directory
stringTEMPORARYParameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringLess common options for the pipeline, typically set in a config file.
Display version and exit.
booleanMethod used to save pipeline results to output directory.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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