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@jvfe jvfe released this 05 Apr 18:12
· 152 commits to master since this release
2.0dev
e00a66b

v2.0 dev - April 5, 2023

Added

  • Adds stubs to every process (2a990d4)

  • Adds assembly as a subworkflow (9e6d267)

  • Adds dbcache (50193b3)

  • Updates documentation

    • README, ROADMAP, CITATIONS, docs/usage.md, docs/output.md

  • Adds test data (c57297a)

  • Reorganizes output directories by subworkflow (ff53e97)

  • Adds option to skip Kraken2 (192ab29)

  • Adds unit tests to ARETE (6a10be0)

  • Adds CI (49eb292)

  • Adds initialization script to the workflow (300f524)

  • Make FastTree the default under the Phylo subwf (b3a3ffa)

  • Adds light parameter to the workflow (b3a3ffa)

  • Concatenate and filter alignment results (8e738ef)

  • Adds PopPUNK (d4ea29e)

  • Updates and improves Bakta, making it the default(3cb354c)

  • Adds DIAMOND alignment against ICEberg2 (ed548cb)

  • Adds IslandPath (0c2ba57)

  • Adds VIBRANT (f0b1f99)

  • Adds Integron Finder (00735d1)

  • Adds Genome subsampling using PopPUNK distances (af41029)

Fixed

  • Makes assembly and assemblyqc entries available (4fd4843)
  • Change databases to value channels so they can be recycled (1285c05)
  • Adds missing params to config and schema (a2c2ea7)
  • Integrate phylo subworkflow to the main pipeline (069400d)

Deprecated

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