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.
| 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'*