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$The file must have a header and can have two columns: "seeds" and "network". If either "seeds" or "network" are missing, the --seeds and --network parameters are expected as replacement.
Path(s) to one or multiple file(s) with seed genes
stringMultiple files have to be "," separated. Each file must have one line per seed gene. This parameter cannot be set, if there is a "seeds" column, in the sample sheet provided via --input.
Path(s) to one or multiple PPI network(s) in gt, csv, graphml, xml, dot, or gml format.
stringMultiple files have to be "," separated.
Type of gene/protein ids
stringThe output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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.
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 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.
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/masterIf 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.
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.
stringThe 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})$An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.
Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Do not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringIncoming hook URL for messaging service. Currently, MS Teams and Slack are supported.
Custom 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