strict-syntax-health/lint_results/prints-help-results/drugresponseeval_help.txt at main · nf-core/strict-syntax-health · GitHub

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$ NXF_SYNTAX_PARSER=v2 nextflow run . --help


 N E X T F L O W   ~  version 26.04.3

Launching `./main.nf` [focused_davinci] revision: ea188be49f

WARN: Unrecognized config option 'validation.defaultIgnoreParams'
WARN: Unrecognized config option 'validation.monochromeLogs'

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                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/drugresponseeval 1.2.2dev
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Typical pipeline command:

  nextflow run nf-core/drugresponseeval -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>

help message of that parameter will be printed.
or `--helpFull`.

Model options
  --models                   [string] Model to be tested. [default: NaiveDrugMeanPredictor]
  --baselines                [string] Baselines to be tested. [default: NaiveMeanEffectsPredictor]

Input/output options
  --run_id                   [string] Run name for the pipeline. The subdirectory in results will be named like this. [default:
my_run]
  --dataset_name             [string] Name of the dataset. Pre-supplied datasets are CTRPv2, CTRPv1, CCLE, GDSC1, GDSC2, TOYv1, TOYv2,
BeatAML2, and PDX_Bruna. [default: CTRPv2]
  --outdir                   [string] The output directory where the results will be saved. Default is results/ [default: results]

  --email                    [string] Email address for completion summary.

Mode options (LPO/LCO/LTO/LDO)
  --test_mode                [string] Run the pipeline in test mode LPO (Leave-random-Pairs-Out), LCO (Leave-Cell-line-Out), or LDO
(Leave-Drug-Out). [default: LCO]

Randomization options
  --randomization_mode       [string] Randomization mode for the pipeline. [default: None]
  --randomization_type       [string] Randomization type for the pipeline.  (accepted: permutation, invariant) [default: permutation]


Robustness options
  --n_trials_robustness      [integer] Number of trials to run for the robustness test [default: 0]

Data options
  --path_data                [string] Path to the data directory. [default: data]
  --measure                  [string] The name of the drug response measure to use.  (accepted: LN_IC50, pEC50, AUC, response, EC50,
IC50) [default: LN_IC50]
  --cross_study_datasets     [string] Datasets for cross-study prediction.
  --zenodo_link              [string] Link to the latest Zenodo version of the dataset. [default:
https://zenodo.org/records/20624451/files/]

Additional options
  --no_refitting             [boolean] 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. [default:
false]
  --optim_metric             [string]  Optimization metric for the pipeline.  (accepted: RMSE, MSE, MAE, R^2, Pearson, Spearman,
Kendall) [default: RMSE]
  --n_cv_splits              [integer] Number of cross-validation splits. [default: 10]
  --response_transformation  [string]  Response transformation  (accepted: None, standard, minmax, robust) [default: None]
  --model_checkpoint_dir     [string]  Model checkpoint directory [default: TEMPORARY]
  --no_hyperparameter_tuning [boolean] Disable hyperparameter tuning. [default: false]
  --final_model_on_full_data [boolean] Train final model on full data. [default: false]

Generic options
  --help                     [boolean, string] Display the help message.
  --help_full                [boolean]         Display the full detailed help message.
  --show_hidden              [boolean]         Display hidden parameters in the help message (only works when --help or --help_full are provided).

 !! Hiding 14 param(s), use the `--showHidden` parameter to show them !!
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* The nf-core framework
    https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
    https://github.com/nf-core/drugresponseeval/blob/main/CITATIONS.md