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$Path(s) to one or multiple file(s) with seed genes
stringPath(s) to one or multiple PPI network(s) in gt, csv, graphml, xml, dot, or gml format.
stringType of gene/protein ids
stringThe output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringParameters for the network expansion algorithms.
Flag for skipping first neighbor
booleanFlag for skipping DOMINO
booleanFlag for skipping Robust
booleanFlag for skipping Robust-bias-aware
booleanFlag for skipping DIAMOnD
booleanDesired number of DIAMOnD genes.
integer200Weight of the seeds.
integer1Flag for skipping random walk with restart
booleanAdd a scaling depending on the node’s degree.
booleanCompute the symmetric instead of column-wise normalized Markov matrix.
booleanDamping factor/restart probability.
number0.8Skip module visualization
booleanIf a module has more nodes it will not be visualized.
integer500Flag for skipping the export to the Drugst.One platform
booleanIf a module has more nodes it will not be exported to the Drugst.One platform. Includes drug prioritization.
integer500Set parameters regarding the annotation.
Flag for skipping the annotation part of the process.
booleanFlag for validating online at baderlab.org.
booleanFlag for adding variants to the biopax annotation file.
booleanFlag skipping the entire evaluation workflow
booleanFlag for skipping g:Profiler
booleanFlag for skipping DIGEST
booleanFlag for skipping only the reference-free mode of DIGEST
booleanFlag for skipping only the reference-based mode of DIGEST
booleanFlag for running the seed permutation-based evaluation
booleanFlag for running the network permutation-base evaluation
booleanNumber of times the network will be permuted for the network permutation-based evaluation
integer100Path(s) to folder(s) with pre-computed permuted networks for the network permutation-based evaluation
stringParameters for the drug prioritization methods.
Flag for running proximity
booleanPath(s) to the shortest path pickle file(s) used for proximity.
stringLocal path to the drug to targets file used for proximity.
stringFlag for skipping drug predictions
booleanDrugst.One parameter for including indirect drugs.
booleanDrugst.One parameter for including non approved drugs.
booleanDrugst.One parameter for defining the maximum number of returned drugs.
integer50Drugst.One parameter for algorithms to be used. Comma separated list. Options: ‘trustrank’, ‘degree’ and ‘closeness’.
stringtrustrankParameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringLess common options for the pipeline, typically set in a config file.
Display version and exit.
booleanMethod used to save pipeline results to output directory.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Do not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringCustom config file to supply to MultiQC.
stringCustom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
stringCustom MultiQC yaml file containing HTML including a methods description.
stringBoolean whether to validate parameters against the schema at runtime
booleantrueBase URL or local path to location of pipeline test dataset files
stringhttps://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