TheiaProk Inputs on Terra

When running tbp-parser as part of the TheiaProk workflow series (find documentation for TheiaProk here) on Terra.bio, an optional input must be activated to instruct TheiaProk to run tbp-parser.

tbp-parser is not on by default due to the nature of this tool and its outputs.

TheiaProk Version

This information only corresponds to the upcoming PHB v2.3.0 release. These inputs and outputs may not be applicable to other versions of TheiaProk.

Required Inputs

To activate tbp-parser you must set the following variable to true:

Terra Task name	Variable	Type	Description	Default Value
merlin_magic	call_tbp_parser	Boolean	Set to true to activate tbp-parser	false

Optional Inputs

The following optional inputs are also available for user modification on Terra:

Terra Task name	Variable	Type	Description	Default Value
merlin_magic	tbp_parser_add_cs_lims	Boolean	Set to true to add Cycloserine (CS) fields to the LIMS report	false
merlin_magic	tbp_parser_coverage_regions_bed	File	A BED file containing the regions to calculate percent coverage for	tbdb-modified-regions.md
merlin_magic	tbp_parser_coverage_threshold	Int	The minimum percentage of a region that has depth above the threshold set by min_depth (used for a gene/locus to pass QC)	100
merlin_magic	tbp_parser_debug	Boolean	Set to false to turn off debug mode for tbp-parser	true
merlin_magic	tbp_parser_docker_image	String	The Docker image to use when running tbp-parser	"us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:2.3.0"
merlin_magic	tbp_parser_etha237_frequency	Float	Minimum frequency for a mutation in ethA at protein position 237 to pass QC in tbp-parser	0.1
merlin_magic	tbp_parser_expert_rule_regions_bed	File	A file that contains the regions where R mutations and expert rules are applied
merlin_magic	tbp_parser_min_depth	Int	Minimum depth for a variant to pass QC in tbp_parser	10
merlin_magic	tbp_parser_min_frequency	Int	The minimum frequency for a mutation to pass QC	0.1
merlin_magic	tbp_parser_min_read_support	Int	The minimum read support for a mutation to pass QC	10
merlin_magic	tbp_parser_operator	String	Fills the "operator" field in the tbp_parser output files	"Operator not provided"
merlin_magic	tbp_parser_output_seq_method_type	String	Fills out the "seq_method" field in the tbp_parser output files	"Sequencing method not provided"
merlin_magic	tbp_parser_rpob449_frequency	Float	Minimum frequency for a mutation at protein position 449 to pass QC in tbp-parser	0.1
merlin_magic	tbp_parser_rrl_frequency	Float	Minimum frequency for a mutation in rrl to pass QC in tbp-parser	0.1
merlin_magic	tbp_parser_rrl_read_support	Int	Minimum read support for a mutation in rrl to pass QC in tbp-parser	10
merlin_magic	tbp_parser_rrs_frequency	Float	Minimum frequency for a mutation in rrs to pass QC in tbp-parser	0.1
merlin_magic	tbp_parser_rrs_read_support	Int	Minimum read support for a mutation in rrs to pass QC in tbp-parser	10
merlin_magic	tbp_parser_tngs_data	Boolean	Set to true to enable tNGS-specific parameters and runs in tbp-parser	false

Find the outputs for tbp-parser in TheiaProk on Terra here.