nf-core/deepmodeloptim
Stochastic Testing and Input Manipulation for Unbiased Learning Systems
Define where the pipeline should find input data.
Input data CSV file
stringData config YAML
stringModel file in Python
stringModel config YAML
stringThe output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringflag to save transformed csv data.If set to true, the transformed data will be saved in the output directory.
booleanEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Files that can be provided as optional input or omitted.
File to be used to initialize the model in tuning
stringOptions for preprocessing the data
Preprocessing config YAML
stringName of iGenomes reference.
stringThe base path to the igenomes reference files
strings3://ngi-igenomes/igenomes/Size of the peak extracted from the BED file
integer300Options for tuning the model
Range of trials for the tuning. Defined as min,max,step.
stringNumber of replicates for the tuning.
integer1Options for evaluating the model
Prediction data CSV file
stringSpecify maximun processes resources
set maximum GPU limit
integer1Container for development stage
stringWhat to do and how to handle errors
Tells the pipeline how to behave on error
stringfinishnumber of time to retry if err_strat is set to retry
integeroptions to skip or change bhaviour of pipeline
checks if all input are comatible and the model can be tuned.
booleantrueoptional flag to do a more/less extensive check during check_model.
stringrun the shuffle sanity check
booleantruedeveloper flag
booleanParameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringLess common options for the pipeline, typically set in a config file.
Display version and exit.
booleanMethod used to save pipeline results to output directory.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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