Define where the pipeline should find input data and save output data.

Path to a CSV sample sheet defining seed file-network combinations

type: string
pattern: ^\S+\.csv$

Path(s) to one or multiple file(s) with seed genes

type: string

Path(s) to one or multiple PPI network(s) in gt, csv, graphml, xml, dot, or gml format.

type: string

Type of gene/protein ids

type: string

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

required
type: string

Email address for completion summary.

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

MultiQC report title. Printed as page header, used for filename if not otherwise specified.

type: string

Parameters for the network expansion algorithms.

Flag for skipping first neighbor

type: boolean

Flag for skipping DOMINO

type: boolean

Flag for skipping Robust

type: boolean

Flag for skipping Robust-bias-aware

type: boolean

Flag for skipping DIAMOnD

type: boolean

Desired number of DIAMOnD genes.

type: integer
default: 200

Weight of the seeds.

type: integer
default: 1

Flag for skipping random walk with restart

type: boolean

Add a scaling depending on the node’s degree.

type: boolean

Compute the symmetric instead of column-wise normalized Markov matrix.

type: boolean

Damping factor/restart probability.

type: number
default: 0.8

Skip module visualization

type: boolean

If a module has more nodes it will not be visualized.

type: integer
default: 500

Flag for skipping the export to the Drugst.One platform

type: boolean

If a module has more nodes it will not be exported to the Drugst.One platform. Includes drug prioritization.

type: integer
default: 500

Set parameters regarding the annotation.

Flag for skipping the annotation part of the process.

type: boolean

Flag for validating online at baderlab.org.

type: boolean

Flag for adding variants to the biopax annotation file.

type: boolean

Flag skipping the entire evaluation workflow

type: boolean

Flag for skipping g:Profiler

type: boolean

Flag for skipping DIGEST

type: boolean

Flag for skipping only the reference-free mode of DIGEST

type: boolean

Flag for skipping only the reference-based mode of DIGEST

type: boolean

Flag for running the seed permutation-based evaluation

type: boolean

Flag for running the network permutation-base evaluation

type: boolean

Number of times the network will be permuted for the network permutation-based evaluation

type: integer
default: 100

Path(s) to folder(s) with pre-computed permuted networks for the network permutation-based evaluation

type: string

Parameters for the drug prioritization methods.

Flag for running proximity

type: boolean

Path(s) to the shortest path pickle file(s) used for proximity.

hidden
type: string

Local path to the drug to targets file used for proximity.

hidden
type: string

Flag for skipping drug predictions

type: boolean

Drugst.One parameter for including indirect drugs.

type: boolean

Drugst.One parameter for including non approved drugs.

type: boolean

Drugst.One parameter for defining the maximum number of returned drugs.

type: integer
default: 50

Drugst.One parameter for algorithms to be used. Comma separated list. Options: ‘trustrank’, ‘degree’ and ‘closeness’.

type: string
default: trustrank

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

File size limit when attaching MultiQC reports to summary emails.

hidden
type: string
default: 25.MB
pattern: ^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$

Do not use coloured log outputs.

hidden
type: boolean

Incoming hook URL for messaging service

hidden
type: string

Custom config file to supply to MultiQC.

hidden
type: string

Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file

hidden
type: string

Custom MultiQC yaml file containing HTML including a methods description.

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