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
--fasta_path	Path to directory containing single sample fasta files	Yes (path as string)
--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)

Run Environment

Param	Description	Input Required
--docker_container	Name of the Docker container	Yes, if running with docker profile (name as string)
--docker_container_vadr	Name of the Docker container to run VADR annotation	Yes, if running with docker profile (name 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)

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)
--val_date_format_flag	Flag to change date output	Yes (-s, -o, or -v as string)
--val_keep_pi	Flag to keep personal identifying info, if provided otherwise it will return an error	Yes (true/false as bool)
--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_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 as bool)
--lift_print_help_exit	Print help and exit the program	Yes (true/false as bool)
--lift_parallel_processes	# of parallel processes to use for liftoff	Yes (Integer)
--lift_delete_temp_files	Deletes the temporary files after finishing transfer	Yes (true/false as string)
--lift_child_feature_align_threshold	Map only if its child features align with sequence identity > this value	Yes (Integer)
--lift_unmapped_feature_file_name	Name of unmapped features file name	Yes (path as string)
--lift_copy_threshold	Minimum sequence identity in exons/CDS for which a gene is considered a copy; must be greater than -s; default is 1.0	Yes (float)
--lift_distance_scaling_factor	Distance scaling factor; by default D =2.0	Yes (float)
--lift_flank	Amount of flanking sequence to align as a fraction of gene length	Yes (float between [0.0-1.0])
--lift_overlap	Maximum fraction of overlap allowed by 2 features	Yes (float between [0.0-1.0])
--lift_mismatch	Mismatch penalty in exons when finding best mapping; by default M=2	Yes (integer)
--lift_gap_open	Gap open penalty in exons when finding best mapping; by default GO=2	Yes (integer)
--lift_gap_extend	Gap extend penalty in exons when finding best mapping; by default GE=1	Yes (integer)
--lift_infer_transcripts	Use if annotation file only includes exon/CDS features and does not include transcripts/mRNA	Yes (True/False as string)
--lift_copies	Look for extra gene copies in the target genome	Yes (True/False as string)
--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, then will use ref gff path to construct one	Yes (N/A or name as string)

VADR

Param	Description	Input Required
--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)

Sample Submission

Param	Description	Input Required
--genbank	Submit to GenBank	Yes (true/false as bool)
--sra	Submit to SRA	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)
--batch_name	Name of the batch to prefix samples with during submission	Yes (name as string)
--send_submission_email	Toggle email notification on/off	Yes (true/false as bool)
--req_col_config	Path to the required_columns.yaml file	Yes (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'*