Parameters¶

Default parameters are given in the nextflow.config file. This table lists the parameters that can be changed to a value, path or true/false. When changing these parameters pay attention to the required inputs and make sure that paths line-up and values are within range. To change a parameter you may change with a flag after the nextflow command or change them within your nextflow.config file.

Please note the correct formatting and the default calculation of submission_wait_time at the bottom of the params table.

Input Files¶

Param	Description	Input Required
--ref_fasta_path	Reference Sequence file path	Yes (path as string)
--meta_path	Meta-data file path for samples	Yes (path as string)
--ref_gff_path	Reference gff file path for annotation	Yes (path as string)

General Subworkflow¶

Param	Description	Input Required
--submission	Toggle for running submission	Yes (true/false as bool)
--annotation	Toggle for running annotation	Yes (true/false as bool)
--cleanup	Toggle for running cleanup subworkflows	Yes (true/false as bool)
--fetch_reports_only	Toggle for only fetching submission reports	Yes (true/false as bool)

General Settings¶

Param	Description	Input Required
--date_format_flag	Flag to specify the date format. Options: s (default, YYYY-MM), v (verbose, YYYY-MM-DD), o (original, unchanged)	Yes (string)
--publish_dir_mode	Mode for publishing directory, e.g., 'copy' or 'move'	Yes (string)
--remove_demographic_info	Flag to remove demographic info. If true, values in host_sex, host_age, race, ethnicity are set to 'Not Provided'	Yes (true/false)

Cleanup Subworkflow¶

Param	Description	Input Required
--clear_nextflow_log	Clears nextflow work log	Yes (true/false as bool)
--clear_work_dir	Param to clear work directory created during workflow	Yes (true/false as bool)
--clear_conda_env	Clears conda environment	Yes (true/false as bool)
--clear_nf_results	Remove results from nextflow outputs	Yes (true/false as bool)

General Output¶

Param	Description	Input Required
--output_dir	File path to submit outputs from pipeline	Yes (path as string)
--overwrite_output	Toggle to overwriting output files in directory	Yes (true/false as bool)

Validation¶

Param	Description	Input Required
--val_output_dir	File path for outputs specific to validate sub-workflow	Yes (folder name as string)
--validate_custom_fields	Toggle checks/transformations for custom metadata fields on/off	No (true/false as bool)
--custom_fields_file	Path to the JSON file containing custom metadata fields and their information	No (path as string)
--validate_params	Flag to enable or disable parameter validation	No (true/false as bool)

Liftoff¶

Param	Description	Input Required
--final_liftoff_output_dir	File path to liftoff specific sub-workflow outputs	Yes (folder name as string)
--lift_print_version_exit	Print version and exit the program	Yes (true/false)
--lift_print_help_exit	Print help and exit the program	Yes (true/false)
--lift_parallel_processes	Number of parallel processes to use for liftoff	Yes (integer)
--lift_child_feature_align_threshold	Map only if its child features align with sequence identity greater than this value	Yes (float)
--lift_unmapped_feature_file_name	Name of unmapped features file	Yes (path as string)
--lift_copy_threshold	Minimum sequence identity in exons/CDS for which a gene is considered a copy; default is 1.0	Yes (float)
--lift_distance_scaling_factor	Distance scaling factor; default is 2.0	Yes (float)
--lift_flank	Amount of flanking sequence to align as a fraction of gene length	Yes (float between 0.0 and 1.0)
--lift_overlap	Maximum fraction of overlap allowed by two features	Yes (float between 0.0 and 1.0)
--lift_mismatch	Mismatch penalty in exons when finding best mapping; default is 2	Yes (integer)
--lift_gap_open	Gap open penalty in exons when finding best mapping; default is 2	Yes (integer)
--lift_gap_extend	Gap extend penalty in exons when finding best mapping; default is 1	Yes (integer)
--lift_minimap_path	Path to minimap if you did not use conda or pip	Yes (N/A or path as string)
--lift_features_database_name	Name of the feature database, if none, will use ref gff path to construct one	Yes (N/A or name as string)
--lift_feature_types	Path to the file containing feature types	Yes (path as string)
--lift_coverage_threshold	Minimum coverage threshold for feature mapping	Yes (float)
--repeatmasker_liftoff	Flag to enable or disable RepeatMasker and Liftoff steps	Yes (true/false)

VADR¶

Param	Description	Input Required
--vadr	Toggle for running VADR annotation	Yes (true/false as bool)
--vadr_output_dir	File path to vadr specific sub-workflow outputs	Yes (folder name as string)
--vadr_models_dir	File path to models for MPXV used by VADR annotation	Yes (folder name as string)

BAKTA¶

Controlling Bakta within TOSTADAS uses parameters of the same name with prefix --bakta_ as described below. For more details, visit the Bakta GitHub page.

Param	Description	Input Required
--bakta_db_path	Path to Bakta database if user is supplying database	No (path to database)
--download_bakta_db	Option to download Bakta database	Yes (true/false)
--bakta_db_type	Bakta database type (light or full)	Yes (string)
--bakta_output_dir	File path to bakta specific sub-workflow outputs	Yes (folder name as string)
--bakta_min_contig_length	Minimum contig size	Yes (integer)
--bakta_threads	Number of threads to use while running annotation	Yes (integer)
--bakta_genus	Organism genus name	Yes (N/A or name as string)
--bakta_species	Organism species name	Yes (N/A or name as string)
--bakta_strain	Organism strain name	Yes (N/A or name as string)
--bakta_plasmid	Name of plasmid	Yes (unnamed or name as string)
--bakta_locus	Locus prefix	Yes (contig or name as string)
--bakta_locus_tag	Locus tag prefix	Yes (autogenerated or name as string)
--bakta_translation_table	Translation table	Yes (integer)
--bakta_gram	Gram type for signal peptide predictions	No ('+' '-' '?')
--bakta	Toggle for running Bakta annotation	Yes (true/false as bool)
--bakta_complete	Complete Bakta annotation	Yes (string)
--bakta_compliant	Compliant with Bakta standards	Yes (true/false)
--bakta_keep_contig_headers	Keep contig headers	Yes (string)
--bakta_proteins	Proteins to include in annotation	Yes (string)
--bakta_replicons	Replicons to include in annotation	Yes (string)
--bakta_skip_cds	Skip CDS annotation	Yes (string)
--bakta_skip_crispr	Skip CRISPR annotation	Yes (string)
--bakta_skip_gap	Skip gap annotation	Yes (string)
--bakta_skip_ncrna	Skip ncRNA annotation	Yes (string)
--bakta_skip_ncrna_region	Skip ncRNA region annotation	Yes (string)
--bakta_skip_ori	Skip origin annotation	Yes (string)
--bakta_skip_plot	Skip plot generation	Yes (true/false)
--bakta_skip_pseudo	Skip pseudogene annotation	Yes (string)
--bakta_skip_rrna	Skip rRNA annotation	Yes (string)
--bakta_skip_sorf	Skip sORF annotation	Yes (string)
--bakta_skip_tmrna	Skip tmRNA annotation	Yes (string)
--bakta_skip_trna	Skip tRNA annotation	Yes (string)

Sample Submission¶

Param	Description	Input Required
--genbank	Submit to GenBank	Yes (true/false as bool)
--sra	Submit to SRA	Yes (true/false as bool)
--biosample	Submit to Biosample	Yes (true/false as bool)
--gisaid	Submit to GISAID	Yes (true/false as bool)
--submission_output_dir	Either name or relative/absolute path for the outputs from submission	Yes (name or path as string)
--submission_prod_or_test	Whether to submit samples for test or actual production	Yes (prod or test as string)
--submission_config	Configuration file for submission to public repos	Yes (path as string)
--submission_wait_time	Calculated based on sample number (3 * 60 secs * sample_num)	integer (seconds)
--send_submission_email	Toggle email notification on/off	Yes (true/false as bool)
--submission_mode	Mode of submission	Yes (string)
--update_submission	Flag to enable or disable updating existing submissions	Yes (true/false as bool)

❗ Important note about send_submission_email: An email is only triggered if Genbank is being submitted to AND table2asn is the genbank_submission_type. As for the recipient, this must be specified within your submission config file under 'general' as 'notif_email_recipient'*

Last update: 2025-03-26