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1.1.0 - British Beans on Toast - 2023-04-27
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@jasmezz jasmezz released this 27 Apr 21:46
· 600 commits to master since this release
1.1.0
1c1c9ae
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v1.1.0 - British Beans on Toast - [2023-04-27]

Added

  • #238 Added dedicated DRAMP database downloading step for AMPcombi to prevent parallel downloads when no database provided by user. (by @jfy133)
  • #235 Added parameter annotation_bakta_db_downloadtype to be able to switch between downloading either full (33.1 GB) or light (1.3 GB excluding UPS, IPS, PSC, see parameter description) versions of the Bakta database. (by @jasmezz)
  • #249 Added bakta annotation to CI tests. (by @jasmezz)
  • #251 Added annotation tool: Pyrodigal. (by @jasmezz)
  • #252 Added a new parameter -arg_rgi_savejson that saves the file <samplename>.json in the RGI directory. The default ouput for RGI is now only <samplename>.txt. (by @Darcy220606)
  • #253 Updated Prodigal to have compressed output files. (by @jasmezz)
  • #262 Added comBGC function to screen whole directory of antiSMASH output (one subfolder per sample). (by @jasmezz)
  • #263 Removed AMPlify from test_full.config. (by @jasmezz)
  • #266 Updated README.md with Pyrodigal. (by @jasmezz)

Fixed

  • #243 Compress the ampcombi_complete_summary.csv in the output directory. (by @louperelo)
  • #237 Reactivate DeepARG automatic database downloading and CI tests as server is now back up. (by @jfy133)
  • #235 Improved annotation speed by switching off pipeline-irrelevant Bakta annotation steps by default. (by @jasmezz)
  • #235 Renamed parameter annotation_bakta_db to annotation_bakta_db_localpath. (by @jasmezz)
  • #242 Fixed MACREL '.faa' issue that was generated when it was run on its own and upgraded MACREL from version 1.1.0 to 1.2.0 (by @Darcy220606)
  • #248 Applied best-practice error("message") to all (sub)workflow files. (by @jasmezz)
  • #254 Further resource optimisation based on feedback from 'real world' datasets. (ongoing, reported by @alexhbnr and @Darcy220606, fix by @jfy133)
  • #266 Fixed wrong process name in base.config. (reported by @Darcy220606, fix by @jasmezz)

Dependencies

Tool Previous version New version
Bakta 1.6.1 1.7.0

Deprecated

Photo by Jon Chan under CC BY-SA 2.0

Contributors

alexhbnr, jfy133, and 3 other contributors
Assets 2
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