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@azat-badretdin azat-badretdin released this Apr 1, 2020

  • Uses pgap 4.11 code base
  • Fix bug causing failure in taxcheck when the genome is assigned to the wrong organism
  • Extension into gaps fix in genemark
Assets 2

@slottad slottad released this Mar 18, 2020 · 1 commit to master since this release

Fixed an annotation error that allowed coding regions to have overlapping tRNAs.

Assets 2

@slottad slottad released this Feb 7, 2020 · 30 commits to master since this release

This release has the following new features:

  • Optional taxonomy checking based upon ANI
  • Support for containers other than Docker, such as Singularity and Podman
  • Self updating for the pgap.py control script
  • Numerous minor improvements to the annotation pipeline
  • Support for running without accessing the Internet (air-gapped)
  • Uses pgap 4.11 code base
Assets 2

@slottad slottad released this Nov 26, 2019 · 153 commits to master since this release

Fix a problem in Find Best Evidence Alignments affecting some users.
Uses pgap 4.10 code base

Assets 2

@slottad slottad released this Nov 11, 2019 · 157 commits to master since this release

Additions required for the NCBI Pathogen surveillance effort.
Uses pgap 4.10 code base

Assets 2

@slottad slottad released this Nov 5, 2019 · 176 commits to master since this release

This release uses an new version of tRNAscan (tRNAscan-SE:2.0.4, Methods Mol Biol. 2019;1962:1-14), and includes our most up-to-date HMM and BlastRule collections for naming proteins.
Uses pgap 4.10 code base.

Assets 2
Oct 3, 2019
remove special treatment of sqlite_cache input, thus making it read-o…
…nly; JIRA: PGAPX-545
Sep 5, 2019
added passing of no_internet flag from wf_common to prepare_user_inpu…
…t2.cwl; also, some OCD indentation to 2-space standard; JIRA: PGAPX-453

@azat-badretdin azat-badretdin released this Aug 27, 2019 · 276 commits to master since this release

Bug fixes:

  • Removed passing bacterial_screening/feats to screen_evaluate: we already analyzed it in fscr_calls_pass1, no need to add unfiltered input from earlier in processing.
  • Fixed the problem that was slowing down logging.
  • FASTA validation now acknowledges user request to ignore all errors.
  • Uses multiprocessor SPARCLBL calculations.
  • Uses pgap 4.9 code base
Assets 2

@slottad slottad released this Aug 6, 2019 · 293 commits to prod since this release

Better error handling.

Assets 2
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