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1.4.2

  • Added an upper version lock to the pipeline, preventing execution with new and untestet versions of nextflow
  • Fixed an issue with Plassembler database installation
  • Updated autocycler to 0.6.2

1.4.0

  • Updated reference database to v1.2
  • Added Autocycler to optionally run consensus assembly for long reads
  • Added Plassembler to default long-read assembly workflows to improve recovery of plasmids when not using Autocycler
  • Moved redundant genome size calculations into its own sub workflow
  • Defaulting genome size estimate to 6MB if calculation fails
  • Medaka polishing: Check if reads contain basecalling model meta data; else skip if model isn't provided via command line
  • Replaced ConfindR db download with proper installation workflow
  • Updated CheckM2 database download to specify a user-agent as a fix to aborting file transfers
  • Adding pipeline settings to sample-level JSON
  • Updated Chopper to version 0.12.0