v3.0.1 - Mended Zooble [23/09/2026]

Warning

This 3.0.0 major release have breaking changes. Samplesheets and command lines written for
v2.0.0 will not work unmodified. See the v3.0.0 changelog notes for details.

Patch release fixing reference genome resolution when --genome is used.

Added

• Added manifest.diagram, pointing at the pipeline metro map so that it is displayed on the
  pipeline's nf-co.re and Seqera Platform pages

Fixed

• Runs using --genome (or any iGenomes key) failed immediately with
  Missing genome. A genome to annotate must be provided with the --fasta or --genome option.,
  even though the parameter summary showed the expected fasta and gtf paths. The iGenomes
  attributes were assigned with params.fasta = getGenomeAttribute('fasta') in main.nf, which
  on the Nextflow versions supported by this pipeline (>= 25.10.4) only populates the entry
  script's parameters: included subworkflows and workflows still saw params.fasta as
  undefined. The reference files are now resolved in the entry workflow, once all config files
  (including those given with -c) are loaded, and passed down explicitly to the ISOSEQ
  workflow instead of being read from params. This also covers a --genome key defined, or
  selected, in a custom config given with -c. Explicit --fasta/--gtf values still take
  precedence over the iGenomes ones. This affected the test_full profile and any user run
  driven by --genome; runs passing --fasta directly (including the test profile) were not
  affected.
• Declared fasta and gtf as pipeline parameters in nextflow.config, removing the
  WARN: Access to undefined parameter messages emitted at startup