Define the models and baselines to be tested.

Model to be tested.

required
type: string
default: NaiveDrugMeanPredictor

Baselines to be tested.

required
type: string
default: NaiveMeanEffectsPredictor

Define 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.

required
type: string
default: my_run

Name of the dataset. Pre-supplied datasets are CTRPv2, CTRPv1, CCLE, GDSC1, GDSC2, TOYv1, TOYv2.

required
type: string
default: CTRPv2

The output directory where the results will be saved. Default is results/

required
type: string
default: results

Email address for completion summary.

type: string
pattern: ^([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).

required
type: string
default: LCO

Options for randomization.

Randomization mode for the pipeline.

type: string
default: None

Randomization type for the pipeline.

type: string

Options for robustness.

Number of trials to run for the robustness test

type: integer

Options for data input.

Path to the data directory.

type: string
default: data

The name of the drug response measure to use.

type: string

Datasets for cross-study prediction.

type: string

Link to the latest Zenodo version of the dataset.

type: string
default: https://zenodo.org/records/15533857/files/
pattern: ^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.

type: boolean

Optimization metric for the pipeline.

type: string

Number of cross-validation splits.

type: integer
default: 10

Response transformation

type: string

Model checkpoint directory

type: string
default: TEMPORARY

Disable hyperparameter tuning.

type: boolean

Train final model on full data.

type: boolean

Parameters used to describe centralised config profiles. These should not be edited.

Git commit id for Institutional configs.

hidden
type: string
default: master

Base directory for Institutional configs.

hidden
type: string
default: https://raw.githubusercontent.com/nf-core/configs/master

Institutional config name.

hidden
type: string

Institutional config description.

hidden
type: string

Institutional config contact information.

hidden
type: string

Institutional config URL link.

hidden
type: string

Less common options for the pipeline, typically set in a config file.

Display version and exit.

hidden
type: boolean

Method used to save pipeline results to output directory.

hidden
type: string

Email address for completion summary, only when pipeline fails.

hidden
type: string
pattern: ^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$

Send plain-text email instead of HTML.

hidden
type: boolean

Do not use coloured log outputs.

hidden
type: boolean

Incoming hook URL for messaging service

hidden
type: string

Boolean whether to validate parameters against the schema at runtime

hidden
type: boolean
default: true

Base URL or local path to location of pipeline test dataset files

hidden
type: string
default: https://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.

hidden
type: string