nf-core/diseasemodulediscovery
A pipeline for network-based disease module identification.
Define where the pipeline should find input data and save output data.
Path to a CSV sample sheet defining seed file-network combinations
string
^\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
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.
string
Multiple files have to be "," separated.
Type of gene/protein ids
string
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
string
Email address for completion summary.
string
^([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.
string
Parameters for the network expansion algorithms.
Flag for skipping first neighbor
boolean
Flag for skipping DOMINO
boolean
Flag for skipping Robust
boolean
Flag for skipping Robust-bias-aware
boolean
Flag for skipping DIAMOnD
boolean
Desired number of DIAMOnD genes.
integer
200
Weight of the seeds.
integer
1
Flag for skipping random walk with restart
boolean
Add a scaling depending on the node's degree.
boolean
Compute the symmetric instead of column-wise normalized Markov matrix.
boolean
Damping factor/restart probability.
number
0.8
Skip module visualization
boolean
If a module has more nodes it will not be visualized.
integer
500
Flag for skipping the export to the Drugst.One platform
boolean
If a module has more nodes it will not be exported to the Drugst.One platform. Includes drug prioritization.
integer
500
Set parameters regarding the annotation.
Flag for skipping the annotation part of the process.
boolean
Flag for validating online at baderlab.org.
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.
boolean
Flag skipping the entire evaluation workflow
boolean
Flag for skipping g:Profiler
boolean
Flag for skipping DIGEST
boolean
Flag for running the seed permutation-based evaluation
boolean
Flag for running the network permutation-base evaluation
boolean
Number of times the network will be permuted for the network permutation-based evaluation
integer
100
Path(s) to folder(s) with pre-computed permuted networks for the network permutation-based evaluation
string
Parameters for the drug prioritization methods.
Flag for running proximity
boolean
Path(s) to the shortest path pickle file(s) used for proximity.
string
Local path to the drug to targets file used for proximity.
string
Flag for skipping drug predictions
boolean
Drugst.One parameter for including indirect drugs.
boolean
Drugst.One parameter for including non approved drugs.
boolean
Drugst.One parameter for defining the maximum number of returned drugs.
integer
50
Drugst.One parameter for algorithms to be used. Comma separated list. Options: 'trustrank', 'degree' and 'closeness'.
string
trustrank
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
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.
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
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.
string
^([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.
boolean
File size limit when attaching MultiQC reports to summary emails.
string
25.MB
^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
Do not use coloured log outputs.
boolean
Incoming hook URL for messaging service
string
Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.
Custom config file to supply to MultiQC.
string
Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
string
Custom MultiQC yaml file containing HTML including a methods description.
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