Define where the pipeline should find input data.

Input data CSV file

type: string

Data config YAML

type: string

Model file in Python

type: string

Model config YAML

type: string

The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.

type: string

flag to save transformed csv data.If set to true, the transformed data will be saved in the output directory.

type: boolean

Email address for completion summary.

type: string
pattern: ^([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

type: string

Options for preprocessing the data

Preprocessing config YAML

type: string

Name of iGenomes reference.

type: string

The base path to the igenomes reference files

hidden
type: string
default: s3://ngi-igenomes/igenomes/

Size of the peak extracted from the BED file

type: integer
default: 300

Options for tuning the model

Range of trials for the tuning. Defined as min,max,step.

type: string

Number of replicates for the tuning.

type: integer
default: 1

Options for evaluating the model

Prediction data CSV file

type: string

Specify maximun processes resources

set maximum GPU limit

type: integer
default: 1

Container for development stage

type: string

What to do and how to handle errors

Tells the pipeline how to behave on error

type: string
default: finish

number of time to retry if err_strat is set to retry

type: integer

options to skip or change bhaviour of pipeline

checks if all input are comatible and the model can be tuned.

type: boolean
default: true

optional flag to do a more/less extensive check during check_model.

type: string

run the shuffle sanity check

type: boolean
default: true

developer flag

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