2.0.1 - 'I was a Teenage Hand Model'

codenamegenerator.com stopped working. Codenames from now on will be song titles.

Added

• #252 Added AGENTS.md

• #233 Update tower.yml with the report paths (the execution trace pattern was fixed in #259, found in review by @Vicbeg).

Fixed

• #248 Retain supplied assemblies without long reads and reject unsupported Jellyfish requests during initialization (@molikd).

• #251 Create the rebgzip output directory in stub runs (@molikd).

• #247 Select available long reads for ONT-only QC while preserving mixed-read choices (@molikd).

• #246 Fixed typo in map creating useless extra field

• #245 Use per-sample models with medaka, instead of params setting.

• #241 Prevent the function create_shortread_channel() in subworkflows/prepare/prepare_shortreads/main.nf from causing concurrent modification exceptions, by creating a fresh map.

• #235 switch qc_reads to hifi if there are no ontreads, see issue #234. Updated handling of parameters not set via samplesheet: the schema no longer sets any defaults, and returns [] for missing keys.