v0.6.2

Fixed

• The de-novo QC stage failing when not a single input read re-aligns against the draft consensus.

v0.6.1

Changed

• More informative warnings for failed samples in the report intro section.

v0.6.0

Added

• Assembly step to de-novo consensus mode to handle longer amplicons. README was updated accordingly.

Removed

• Default local executor CPU and RAM limits

v0.5.0

Changed

• Names of barcoded directories in the sample sheet now need to be of format barcodeXY.

Added

• Support for specifying reference sequences for individual samples with an extra "ref" column in the sample sheet.

v0.4.1

Changed

• The workflow now also emits VCF index files as well as BAM / VCF index files for combined outputs when running with --combine_results.

Fixed

• Emitting an empty consensus FASTA file when consensus generation failed in certain situations. Instead, no file is emitted.
• Now uses the downsampled BAM for medaka annotate.

Removed

• Misleading allelic balance statistic in report.

v0.4.0

Added

• Running the workflow without a reference will switch the workflow to "no-reference mode" and will use SPOA to construct a consensus sequence de novo.

v0.3.5

Changed

• The workflow now also outputs BAM index files.

v0.3.4

Changed

• The workflow now downsamples reads for each amplicon to be in the suitable depth range for Medaka.

v0.3.3

Added

• MacOS ARM64 support.

v0.3.2

Changed

• Updated Medaka to 1.9.1.