ncov-tools v1.9.1

• Enhancement to support pangolin option --analysis-mode (credit: @DarianHole) using a default of accurate

ncov-tools v1.9.0

• Support for Pangolin v4 and backwards compatibility with Pangolin v3 using pangolin_version: "3" in the config.yaml file (by default supports version 4)
• Fixed Dockerfile issue updating pip package to pyvcf3
• Requires the ncov-parser v0.7.0 for inclusion of the scorpio_notes column in the *_summary_qc.tsv file

ncov-tools v1.8.0

• Added support for ARTIC V4 primer schemes, requires an additional parameter in the run config.yaml file. Note that the V3 primer prefix (i.e. "nCoV-2019") is the default if this parameter is missing.

primer_prefix: "SARS-CoV-2"

• Added a new rule for indexing the reference file if it does not already exist

ncov-tools v1.7.1

Fixed the column width in the Flagged Samples table to prevent overlapping columns in Pangolin Notes

ncov-tools v1.7

Added support for Pangolin 3.0.

ncov-tools v1.6

• Improved VOC reporting in the summary report

• ability to configure output directory using the output_dir in the config.yaml file

• ability to identify variants that disrupt amplicons in qc_annotation/<prefix>.primer_snp_depth_summary.tsv

ncov-tools v1.5.1

Added support for multiple snpEff version databases to resolve issue #74

ncov-tools v1.5

• added the -noLog argument to snpEff to prevent sending usage statistics to snpEff

ncov-tools v1.4

• Generates a watchlist report for variants of concern (VOC)
• Updated summary report to include a table with VOCs and lineage
• Updated the summary_qc.tsv file to include VOCs, lineage and frameshift annotations from SNPEff

ncov-tools v1.3.1

Fixed the parasail-python conda package in the environments file