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.
booleanBoolean 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 containing a pre-downloaded Bakta database, or one published by a previous run of this pipeline (only used when annotation_tool=‘bakta’). If unset, the database is downloaded automatically into <outdir>/databases/bakta on first use and reused from there by later runs that point --bakta_db at the same <outdir>/databases/bakta.
stringBakta database type to download
stringMinimum contig length for annotation and analysis
integer200Options for required databases
Directory containing a pre-downloaded Pfam database, or one published by a previous run of this pipeline (only used when skip_traitar=false). If unset, the database is downloaded automatically into <outdir>/databases/pfam on first use and reused from there by later runs that point --pfamdb at the same <outdir>/databases/pfam.
stringOptions 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 containing pre-downloaded MacSyFinder models, or ones published by a previous run of this pipeline (one subdirectory per macsyfinder_models value). If unset, models are downloaded automatically into <outdir>/databases/macsyfinder on first use and reused from there by later runs that point --macsyfinder_db at the same <outdir>/databases/macsyfinder.
stringSkip 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 example file.
stringSkip Gapseq pathway analysis and metabolic modeling
booleantrueDirectory containing a pre-downloaded gapseq reference sequence database (a ‘Bacteria’ subdirectory, as produced by gapseq update-sequences -D <dir>). If present, the live Zenodo download is skipped - set this to a pre-downloaded copy if your compute nodes lack outbound internet access to Zenodo. If unset, defaults to <outdir>/databases/gapseq.
stringCustom arguments for the simplified gapseq doall search step. Only used in the default doall workflow - ignored if any of the gapseq_find_args, gapseq_findtransport_args, gapseq_draft_args, gapseq_medium_args, or gapseq_fill_args below are set, since that switches to the custom/stepwise workflow instead.
string-b 200 -A diamondCustom arguments for ‘gapseq find’ - pathway prediction (default: ‘-b 200 -A diamond’)
stringCustom arguments for ‘gapseq find-transport’ - transporter prediction (default: ‘-b 200’)
stringCustom arguments for ‘gapseq draft’ - draft model construction (default: none)
stringCustom arguments for ‘gapseq medium’ - add/remove specific compounds on top of the predicted medium, e.g. ‘-c “cpd00007:0”’ to remove oxygen (default: none; ignored for samples with their own medium_gapseq_csv file)
stringCustom arguments for ‘gapseq fill’ - gap-filling (default: none)
stringSkip MEMOTE metabolic model quality evaluation (only runs when skip_gapseq=false or skip_carveme=false)
booleantrue