v1.9.1.1

• First release to be compatible with nextflow v23.10+
• Implemented/Fixed GitHub Actions testing workflow, including testing on nextflow v23.10.1 (#46)
• New versioning scheme intended to match versioning of ncov-tools, with additional digit for patches of this pipeline while still using the same version of ncov-tools.

v1.9.0

• Uses ncov-tools v1.9.1 by default (Issue #56)
• Compatible with new versions of pangolin (+v3)
• Inverted defaults for choosing which consensus and variants files to use. Freebayes-generated consensus and variants files are used by default, instead of ivar-generated files. (use --ivar_consensus and --ivar_variants to override)
• Splitting by plate is now default behavior (use --no_split_by_plate to override)
• Using downsampled bams is now default behavior (use --pre_downsampled to override)

v1.5.8

• Use nCoV-2019.bed file instead of nCoV-2019.primer.bed (Issue #54). This change is being made to coincide with the release of BCCDC-PHL/artic-ncov2019 v2.3, where the nCoV-2019.bed file is now a symlink to to the file that is intended for analysis.

v1.5.7

• Fixed issue where the run_name in the qc_reports/summary_qc.tsv file was appended with an underscore (Issue #52)

v1.5.6

• Added flag --primer_scheme_name that allows the user to specify an alternate primer scheme. Default scheme is 'Freed et al.' 1200bp aka 'V1200'. (Issue #49)

v1.5.5

• Make pangolin updates optional (Issue #47)

v1.5.4

• Fix issue where negative control sample was not being found, resulting in no negative control report (Issue #42)

v1.5.3

• Automatically update pangolin on every pipeline invocation (Issue #40)

v1.5.2

• Fix issue where ncov-watch summary files were not populated with data (Issue #38)

v1.5.1

• Add two new parameters: --freebayes_consensus and --freebayes_variants. When used, the consensus and/or variants outputs from freebayes will be used instead of the ivar outputs. (Note: freebayes outputs are only produced by BCCDC-PHL/ncov2019-artic-nf v1.3.0 or later).