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.