Adding tbp-parser to TheiaProk

[sage-wright]

Closes #96 🎉

🛠️ Changes Being Made

• created the tbp-parser repository that implements the expert rules for interpreting the outputs of TBProfiler and added that to a new task
• changed the default variant caller in TBProfiler from bcftools to freebayes.
• added the changes Ash O'Farrell introduced in TBProfiler: Fix minor bug; output median cov, % unmapped #176

🧠 Context and Rationale

This is an adjustment & improvement to the very large single-task Python code that was exceeding 1000 lines. Unit tests have been implemented, functionality has been tested, many bugs squashed.

📋 Workflow/Task Steps

Removes the following tasks:

• tasks/species_typing/task_tb_gene_coverage.wdl
• tasks/species_typing/task_tbprofiler_output_parsing.wdl

Adds the following task:

• tasks/species_typing/task_tbp_parser.wdl

This task runs the tbp-parser Python tool.

Inputs

New optional inputs:

• tbprofiler_output_seq_method_type -> tbp_parser_output_seq_method_type: default="WGS"
• tbprofiler_operator -> tbp_parser_operator
• tbp_parser_min_depth: default=10
• tbp_parser_coverage_threshold: default=100
• tbp_parser_debug: default=false
• tbp_parser_docker_image: default="us-docker.pkg.dev/general-theiagen/theiagen/tbp-parser:0.0.5"

Outputs

New outputs:

• File? tbprofiler_lims_report_csv -> tbp_parser_lims_report_csv
• File? tbprofiler_looker_csv -> tbp_parser_looker_report_csv
• File? tbprofiler_laboratorian_report_csv -> tbp_parser_laboratorian_report_csv
• File? tbprofiler_resistance_genes_percent_coverage -> tbp_parser_coverage_report
• Float? tbp_parser_genome_percent_coverage
• String? tbp_parser_version
• String? tbp_parser_docker

🧪 Testing

Locally

Terra

Testing ongoing.

🔬 Quality checks

Pull Request (PR) checklist:

• Include a description of what is in this pull request in this message.
• The workflow/task has been tested locally and on Terra
• The CI/CD has been adjusted and tests are passing
• Everything follows the style guide

[sage-wright]

Included in #192