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$

The file must have a header and can have two columns: "seeds" and "network". If either "seeds" or "network" are missing, the --seeds and --network parameters are expected as replacement.

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

type: string

Multiple files have to be "," separated. Each file must have one line per seed gene. This parameter cannot be set, if there is a "seeds" column, in the sample sheet provided via --input.

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

type: string

Multiple files have to be "," separated.

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.

type: string

Email address for completion summary.

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

Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (~/.nextflow/config) then you don't need to specify this on the command line for every run.

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 running the BioPAX validator client, i.e. validating at the baderlab server. If "false" will load OBO files locally, which can take some time but is recommended for files > 100Mb.

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 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

If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.

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

The Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.

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})$

An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.

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

Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.

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