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Parameters
RamiyapriyaS edited this page Jan 18, 2024
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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 standard_params.config or standard.yaml 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 |
---|---|---|
--fasta_path | Path to fasta file | 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) |
--db_path | Path to Bakta reference database | Yes (path as string) |
--env_yml | Path to environment.yml file | Yes (path as string) |
Param | Description | Input Required |
---|---|---|
--scicomp | Flag for whether running on Scicomp or not | Yes (true/false as bool) |
--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) |
--docker_container_bakta | Name of the Docker container to run Bakta annotation | Yes, if running with docker profile (name as string) |
Param | Description | Input Required |
---|---|---|
--run_submission | Toggle for running submission | Yes (true/false as bool) |
--run_liftoff | Toggle for running liftoff annotation | Yes (true/false as bool) |
--run_vadr | Toggle for running vadr annotation | Yes (true/false as bool) |
--run_bakta | Toggle for running Bakta annotation | Yes (true/false as bool) |
--cleanup | Toggle for running cleanup subworkflows | Yes (true/false as bool) |
Param | Description | Input Required |
---|---|---|
--clear_nextflow_log | Clears nextflow work log | Yes (true/false as bool) |
--clear_nextflow_dir | Clears nextflow working directory | 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) |
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) |
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) |
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 | Only if its child features usually exons/CDS align with sequence identity ≥S | designate a feature mapped |
--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) |
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) |
Param | Description | Input Required |
---|---|---|
--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) |
Param | Description | Input Required |
---|---|---|
--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_only_meta | Full path directly to the dirs containing validate metadata files | Yes (path as string) |
--submission_only_gff | Full path directly to the directory with reformatted GFFs | Yes (path as string) |
--submission_only_fasta | Full path directly to the directory with split fastas for each sample | Yes (path 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) |
--processed_samples | Path to the directory containing processed samples for update only submission entrypoint (containing <batch_name>.<sample_name> dirs) | 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'