nf-core/deepmodeloptim
Stochastic Testing and Input Manipulation for Unbiased Learning Systems
Define where the pipeline should find input data.
Input data CSV file
string
Data config YAML
string
Model file in Python
string
Model config YAML
string
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
string
flag to save transformed csv data.If set to true, the transformed data will be saved in the output directory.
boolean
Email 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
string
Options for preprocessing the data
Preprocessing config YAML
string
Name of iGenomes reference.
string
The base path to the igenomes reference files
string
s3://ngi-igenomes/igenomes/
Size of the peak extracted from the BED file
integer
300
Options for tuning the model
Range of trials for the tuning. Defined as min,max,step.
string
Number of replicates for the tuning.
integer
1
Options for evaluating the model
Prediction data CSV file
string
Specify maximun processes resources
set maximum GPU limit
integer
1
Container for development stage
string
What to do and how to handle errors
Tells the pipeline how to behave on error
string
finish
number of time to retry if err_strat is set to retry
integer
options to skip or change bhaviour of pipeline
checks if all input are comatible and the model can be tuned.
boolean
true
optional flag to do a more/less extensive check during check_model.
string
run the shuffle sanity check
boolean
true
developer flag
boolean
Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
string
master
Base directory for Institutional configs.
string
https://raw.githubusercontent.com/nf-core/configs/master
Institutional config name.
string
Institutional config description.
string
Institutional config contact information.
string
Institutional config URL link.
string
Less common options for the pipeline, typically set in a config file.
Display version and exit.
boolean
Method used to save pipeline results to output directory.
string
Email 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.
boolean
Do not use coloured log outputs.
boolean
Incoming hook URL for messaging service
string
Boolean whether to validate parameters against the schema at runtime
boolean
true
Base URL or local path to location of pipeline test dataset files
string
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.
string