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)
--dry_run	Simulate submission and print a log.	No (true/false)
--workflow	Specifies the workflow to execute, allowing users to choose the appropriate processing method.	Yes (string)

Workflow Options¶

The following workflows are available for the --workflow parameter:

biosample_and_sra: Runs a submission to BioSample and SRA.
genbank: Runs a GenBank submission.
fetch_accessions: Fetches reports and updates the metadata file.
full_submission: Executes BioSample and SRA submissions, waits 60 seconds multiplied by params.batch_size, fetches reports, updates the metadata file with accession IDs, and then performs the GenBank submission.
update_submission: Executes a BioSample submission using an updated metadata Excel file.

Note: The GenBank submission cannot complete without a BioSample accession ID.

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)
--batch_size	The number of samples to prepare in one submission file.	No (integer)

General Output¶

Param	Description	Input Required
--outdir	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)
--final_submission_outdir	Either name or relative/absolute path for the final outputs from submission report fetching	No (string or path)

Validation¶

Param	Description	Input Required
--validation_outdir	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)

Liftoff¶

Param	Description	Input Required
--final_liftoff_outdir	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_features_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_feature_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_outdir	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_. For more details, visit the Bakta GitHub page.

Param	Description	Input Required
--bakta	Toggle for running Bakta annotation	Yes (true/false as bool)
--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_outdir	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 ('+' '-' '?')
--save_reference	Option to save the downloaded Bakta database	No (true/false)

Sample Submission¶

Param	Description	Input Required
--biosample	Submit to BioSample	Yes (true/false as bool)
--sra	Submit to SRA	Yes (true/false as bool)
--submission_outdir	Either name or relative/absolute path for the outputs from submission	Yes (name or path as string)
--final_submission_outdir	Either name or relative/absolute path for the final outputs from submission report fetching	No (string or path)
--prod_submission	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¶

| --original_submission_outdir | Either name or relative/absolute path for the outputs from original submission (the one being updated) | Yes (name or path as string) |

❗ 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: 2025-09-12