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
stringDirectory to cache the Bakta database in (only used when annotation_tool=‘bakta’). Downloaded automatically on first use via Nextflow’s storeDir and reused on subsequent runs, so most users never need to set this.
stringassets/bakta_dbBakta database type to download
stringMinimum contig length for annotation and analysis
integer200Options for required databases
Directory to cache the Pfam database in (only used when skip_traitar=false). Downloaded automatically on first use via Nextflow’s storeDir and reused on subsequent runs, so most users never need to set this.
stringassets/pfam_dbOptions for functional annotation and metabolic modeling tools
Skip MacSyFinder macromolecular systems detection
booleanMacSyFinder models to use (TXSS for Type III/IV/VI secretion systems)
stringTXSSMacSyFinder –db-type: ‘unordered’ for MAGs/draft assemblies with unreliable gene order (default, most permissive), ‘ordered_replicon’ for a single complete/nearly-complete genome (enables synteny-aware detection), or ‘gembase’ for multiple complete replicons in one gembase-formatted database
stringDirectory to cache downloaded MacSyFinder models in (one subdirectory per macsyfinder_models value). Downloaded automatically on first use via Nextflow’s storeDir and reused on subsequent runs.
stringassets/macsyfinder_dbSkip TRAITAR phenotype prediction
booleanSkip CarveMe genome-scale metabolic reconstruction
booleanPath to CarveMe media database TSV file (columns: medium, description, compound, name). If not provided, uses CarveMe’s default media database. See assets/medium_carveme_mediadb_example.tsv for an example.
stringSkip Gapseq pathway analysis and metabolic modeling
booleantrueCustom arguments for the simplified ‘gapseq doall’ search step (default: ‘-b 200 -A diamond’). Only used in the default doall workflow - ignored if any of the gapseq_find_args/gapseq_findtransport_args/gapseq_draft_args/gapseq_medium_args/gapseq_fill_args below are set, since that switches to the custom/stepwise workflow instead.
stringCustom arguments for ‘gapseq find’ (e.g., ‘-b 200 -A diamond’)
stringCustom arguments for ‘gapseq find-transport’ (e.g., ‘-b 200’)
stringCustom arguments for ‘gapseq draft’ (e.g., ‘-u 200’)
stringCustom arguments for ‘gapseq medium’
stringCustom arguments for ‘gapseq fill’ (e.g., ‘-b 100’)
stringSkip MEMOTE metabolic model quality evaluation (only runs when skip_gapseq=false or skip_carveme=false)
booleantrue