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1.4.0

  • Updated reference database to v1.2
  • Added Autocycler to optionally run consensus assembly for long reads
  • 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
  • Replaced Chopper with Fastplong (faster, compatible with MultiQC)
  • Removed read downsampling with RASUSA as all assembly tools/chains already take care of that
  • Updated CheckM2 database download to specify a user-agent as a fix to aborting file transfers
  • Adding pipeline settings to sample-level JSON