nf-core/bacmodel
Systems-based bacterial functional modeling pipeline
Define where the pipeline should find input data and save output data.
Path to comma-separated or tab-separated file containing information about the samples in the experiment.
string^\S+\.(csv|tsv)$The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Parameters 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.
booleanDo not use coloured log outputs.
booleanIncoming hook URL for messaging service
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.
stringDisplay the help message.
boolean,stringDisplay the full detailed help message.
booleanDisplay hidden parameters in the help message (only works when —help or —help_full are provided).
booleanOptions for genome annotation
Tool to use for genome annotation
stringPath to Bakta database (required if annotation_tool=‘bakta’)
stringDownload Bakta database automatically
booleanArguments for Bakta database download
string--type lightOptions for required databases
Path to Pfam database (required if run_traitar=true)
stringDownload Pfam database automatically
booleanOptions for functional annotation and metabolic modeling tools
Run MacSyFinder for macromolecular systems detection
booleantrueMacSyFinder models to use (TXSS for Type III/IV/VI secretion systems)
stringTXSSRun TRAITAR for phenotype prediction
booleantrueRun CarveMe for genome-scale metabolic reconstruction
booleantrueRun Gapseq for pathway analysis and metabolic modeling
boolean