v2.1.0

This minor release modifies the pangolin task to ensure compatibility with Pangolin ≥v4.0.4

NOTE: In order to incorporate Pangolin ≥v4.0.4, modifications were made that render our SARS-CoV-2 genomics characterization workflows (e.g. TheiaCoV_Illumina_PE) incompatible with older versions of Pangolin.

• Default docker image for pangolin4 task set to: quay.io/staphb/pangolin:4.0.4-pdata-1.2.133

Other Modifications:

New Features

• An s_gene_percent_coverage calculation was added to all Theia_COV workflows for SARS-CoV-2 genomic characterization that incorporate an alignment step (TheiaCoV_ClearLabs, TheiaCoV_Illumina_PE, TheiaCoV_Illumina_SE, and TheiaCoV_ONT).
  • An additional TSV file is made that includes the percent coverage of all genes in SC2 genomes, assuming Wuhan-1 reference genome positions. It can be found under this column: percent_gene_coverage
• A min_depth input variable was created for TheiaCoV_Illumina_PE and TheiaCoV_Illumina_SE workflows to specify the minimum depth of coverage required to call a base in the final assembly output and a variant in the VCF output.
  • The default value for min_depth is 100.
  • This parameter replaces min_depth parameter for two previous tasks consensus and variant_call. These variables have been consolidated.
• The NextClade dataset tag used is now an output value generated in our SARS-CoV-2 genomics characterization workflows (e.g. TheiaCoV_Illumina_PE) under column: nextclade_ds_tag.
• The TheiaCoV_Augur_Run merged_metadata output file is now in CSV format to be compatible with both Auspice and MicrobeTrace.

Default Docker Image Updates

• Default Nextclade docker image updated to: nextstrain/nextclade:1.11.0
• Default nextclade_dataset_tag updated to: 2022-03-31T12:00:00Z
• Default Freyja docker image updated to: quay.io/staphb/freyja:1.3.2

Bug Fixes

• The output of several Mercury files were called CSV files when they were actually TSV files. This is fixed. #112

Pull Requests and Resolved Issues

• added sed line (#115) by @sage-wright in #118
• update docs by @kevinlibuit in #120
• Percent gene coverage calculations by @sage-wright in #126
• converted derived_cols.tsv to a csv file by @sage-wright in #125
• Various patches by @kevinlibuit in #127
• pangolin v4 & updating nextclade defaults across 6 workflows by @kapsakcj in #128
• Update to Freyja v1.3.4 by @kevinlibuit in #130
• Cjk pangolin v4 dev by @kapsakcj in #131
• update default pangolin docker image to 4.0.4 by @kapsakcj in #132
• Update task_versioning.wdl by @kevinlibuit in #134

Full Changelog: v2.0.0...v2.1.0