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 PHB v2.2.0. 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 | Default value | Description |
|---|---|---|---|---|
merlin_magic |
tbprofiler_additional_outputs |
Boolean | false |
Set to true to activate tbp-parser |
Optional Inputs¶
The following optional inputs are also available for user modification on Terra:
| Terra Task name | Variable | Type | Default value | Description |
|---|---|---|---|---|
merlin_magic |
tbp_parser_output_seq_method_type |
String | "WGS" | Fills out the “seq_method” field in the tbp_parser output files |
merlin_magic |
tbp_parser_operator |
String | "Operator not provided" | The operator who ran the analysis; used in the LIMS & Looker reports |
merlin_magic |
tbp_parser_min_depth |
Int | 10 | The minimum depth of coverage required for a site to pass QC |
merlin_magic |
tbp_parser_min_frequency |
Int | 0.1 | The minimum frequency for a mutation to pass QC (0.1 -> 10%) |
merlin_magic |
tbp_parser_min_read_support |
Int | 10 | The minimum read support for a mutation to pass QC |
merlin_magic |
tbp_parser_coverage_threshold |
Int | 100 | The minimum percentage of a region that has depth above the threshold set by min_depth (used for a gene/locus to pass QC) |
merlin_magic |
tbp_parser_coverage_regions_bed |
File | tbdb-modified-regions.md | A BED file containing the regions to calculate percent coverage for |
merlin_magic |
tbp_parser_debug |
Boolean | false | Turn on debug mode for tbp-parser |
merlin_magic |
tbp_parser_add_cs_lims |
Boolean | false | Adds Cycloserine (CS) fields to the LIMS report |
merlin_magic |
tbp_parser_docker_image |
String | "us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:1.6.0" | The Docker image to use when running tbp-parser |