v1.4.5

Changed

• Reconciled workflow with wf-template v5.3.4.

v1.4.4

Changed

• Updated Dorado to v0.9.0

v1.4.3

Changed

• Reconciled workflow with wf-template v5.3.3.

v1.4.2

Added

• q-score filter added to signal ingress.

Changed

• Updated Dorado to v0.8.3
• Reconciled workflow with wf-template v5.3.1.

v1.4.1

Changed

• Reconciled workflow with wf-template v5.3.0.
• Updated Dorado to v0.8.1

v1.4.0

Added

• IGV configuration file with --ref --igv options and either --output_fmt bam or --output_fmt cram.
• Support for gzipped reference genomes.
• output_fmt selects the output format for basecalled and aligned files.

Changed

• Updated Dorado to v0.8.0
• Reconciled workflow with wf-template v5.2.6.
• Do not emit the reference FASTA file.
• Collapse redundant RG and PG header lines when emitting BAM or CRAM.

Fixed

• Workflow starting with --duplex --barcode_kit, despite duplex not supporting barcoding.
• Workflow crashing with --ref {{ reference }} --barcode_kit.
• Aligned reads will no longer be trimmed when demuxing to preserve mapping information.
• Workflow emits confusing warning about Bonito filtering when using Dorado.

Removed

• fastq_only and output_bam options replaced by output_fmt.
  • --output_fmt fastq can be used to output unaligned FASTQ instead of unaligned CRAM.
  • --output_fmt bam can be used to output unaligned or aligned BAM instead of CRAM.

v1.3.0

Added

• Modified base calling with --duplex.
• APK 5.0.0 model.

Changed

• Updated Dorado to v0.7.2 (see https://github.com/nanoporetech/dorado/releases/tag/v0.7.2)

v1.2.2

Changes

• Bug fix for downstream workflows and --poly_a_config which does not affect normal workflow use.

v1.2.1

Added

• Output channel for demuxed BAM files for downstream use.

v1.2.0

### Added

• Support for dorado demux to demultiplex barcoded runs. Specify your --barcode_kit to activate demultiplexing.
• Support for poly(a) tail length estimation with --poly_a_config. You can configure by providng a TOML file to --poly_a_config which is described in detail here

Changed

• Updated Dorado to v0.7.1 (see https://github.com/nanoporetech/dorado/releases/tag/v0.7.1)