v1.2.2

Bug Fixes:

• Augur prep pango_lineages not recognized by augur; reverted back to pangolin_lineages header
• Ensure percent_reference_coverage calculated by unambiguous bases only
• Add percent primer trim to output
• Add BioProject Accession to GenBank metadata file (Mercury Prep workflows)

v1.2.1

Bug Fixes:

• pangolin tasks now use 4 cpus, not 40
• Pangolin Update write to proper output column ("pango_lineage")
• Ensure all outputs for Titan output namings in sync
• Update GenBank metadata formatting to match NCBI standards (Mercury Prep workflows)
• Add local tests wdl file for Titan Illumina PE
• Create test dir with template configs
• Add clock rate and std dev as optional input to Augur Run

v1.2.0

Minor updates:

• Address issue with ivar trim & improperly-formatted bed files
  -- Update ivar docker tag
  -- Make bed file required input for Titan_Illumina_PE
• Change output headers to sync with Broad

v1.1.1

• Fix issue with sample exclusion in Titan_Auspice_Run output
• Remove comment blocks from sarscov2_nextstrain_modified

v1.1.0

New workflows:

• Titan_Augur_Prep: workflow to prepare SC2 sample metadata file for Augur analysis
• Titan_Augur_Run: workflow for SC2 cluster investigations. Titan_Augur_Run will run Augur without a subsampling module using a modified version of the Braod's sarscov2_nextstrain WDL workflow to create an Auspice JSON file; output from the modified sarscov2_nextstrain workflow will also be used to infer SNP distances and create a static PDF report
• Pangolin_Update: Run pangolin on samples with a specified docker image

Modified workflows:

• Mercury Batch: must provide samplename array to enable output that describes which samples were batched and excluded for each repository (batched_samples.tsv and excluded_samples.tsv)

v1.0.1

Bug fixes and unnecessary code removed

• Fixed issue with Mercury batch and inclusion of samples with >0 vadr alerts
• Removed variant_num output in Titan workflows and unnecessary echo statements

v1.0

First stable release of Titan and Mercury workflows

v0.2.1

Fix header issue in metadata_upload files

v0.2

Added the Titan and Mercury workflows

v0.1

First stable dev release