New output columns from TBProfiler Task

[cimendes]

Motivation

This PR adds a new behaviour, controlled by the tbprofiler_additional_outputs boolean (currently set to true) that controls 5 new outputs: tb_profiler_variant_gene_name, tb_profiler_variant_locus_tag, tb_profiler_variant_substitutions, tb_profiler_sequencing_method, tbprofiler_additional_outputs_csv and tbprofiler_laboratorian_csv.

These columns include information in all mutations found by tbprofiler with the following criteria:

• who catalogue associated with resistance, uncertain, and interim (not associated with resistance not included)
• mutation is not synonymous
• ALL mutations in katG, pncA, rpoB, ethA and gid included, except for synonymous mutations

Main changes

• tbprofiler container image was updated to staphb/tbprofiler:4.4.2
• The following new output columns were included with information about each mutation in a comma-delimited list to be ingested into a BigQuery database for visualization in a Looker Dashboard:
  • Column1: tbprofiler_variant_gene_name
  • Column2: tbprofiler_variant_locus_tag
  • Column3: tbprofiler_variant_substitutions in the format mutation_type:nt_sub(aa_sub
  • Column4: tbprofiler_sequencing_method
  • Column5: CSV file to be ingested into CDPH LIMS system with all the information above split into different columns
  • Column6: CSV file to be human readable with the same information as above, and additionally the depth of coverage, the frequency, and a warning if the coverage is below a threshold of 10 times.

Testing

• tbprofiler_additional_outputs set to true
  • Theiaprok_Illumina_SE with 100 samples
  • Theiaprok_Illumina_PE with 100 samples

[cimendes]

Test with commit hash 1af02af

• 100 PE Samples: https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Mendes_Sandbox/job_history/0392d1d4-8999-453d-b07f-df79fa777de8
• 100 SE Samples: https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Mendes_Sandbox/job_history/2c06b0ae-7be9-4b46-8c13-f05e37aa837b