fmalmeida/bacannot v3.3.3

Release Notes

• [#118]
  • Add a parameter to allow user to skip INTEGRON_FINDER execution.
  • Add a parameter to allow user to skip CIRCOS execution.
• Split antismash docker image, and added some snippets to fix some workarounds to allow pipeline to run with singularity

fmalmeida/bacannot v3.3.2

Release changes

v3.3.2 [09-February-2024]

• [#116] -- Small update to avoid having integron_finder gbks with start position as 0, since it breaks conversion to gff.

fmalmeida/bacannot v3.3.1

Release notes

v3.3.1 [29-October-2023]

• [#111] -- Updated falmeida-py package version to fix problem with missing key for Summary.

fmalmeida/bacannot v3.3

Release notes

v3.3 [01-October-2023]

• [#50] -- Add Integron Finder tool to the pipeline
• [#69] -- Change how tools use docker images in order to:
  • make tools use public bioconda images whenever possible to allow easy addition of tools and avoid much conflicts in docker images
  • dimish the size and tools inside the docker images, the docker images now are only built to contain tools and all required for modules that cannot just use bioconda docker images.
• [#81] -- Add MOB Suite tool to the pipeline
• [#85] -- Include checkup on header size for Prokka
• [#98] -- Add ICEberg and PHAST blastp results to json summary
• [#100] -- Update pipeline to use docker shasum instead of tags
• [#107] -- Add a parameter, --enable_deduplication for deduplicating input reads before assembly
• Update unicycler docker image to latest '0.5.0--py310h6cc9453_3' to avoid errors originated from previous image containing buggy installation.
• Other minor changes / updates highlited in [#93]

fmalmeida/bacannot v3.2

Release notes

v3.2 [19-December-2022]

• Fixes #68 reported by @lam-c
  • required a small fix in the scripts used to generated the shiny app
  • thus, new docker image
• Fixes #70
  • Adds a CIRCOS plot of main annotation results
  • For now it is very minimum and will be gradually enhancement in following versions. It contains:
    • forward features
    • reverse features
    • rRNA
    • tRNA
    • AMRFinderPlus and VFDB annotated genes (as labels)
    • PhiSpy annotated prophages
    • GC Skew
• Pipeline also outputs an annotation summary of the main results in JSON format

fmalmeida/bacannot v3.1.7

Release notes

v3.1.7 [6-December-2022]

• Fixes #75 reported by @sunitj, who highlighted that bakta tool required an update.
• Now, as a consequence, the non-core tools, namely Bakta, Flye and Unicycler that are used only when required in particular cases now have a parameter to control the version of the tool desired.
  • These non-default tools are used with bioconda images from quay.io, now they have parameters --bakta_version, --unicycler_version and --flye_version that allows users to control the version (from quay.io) used.
• PR: #76

fmalmeida/bacannot v3.1.6

Release notes

v3.1.6 [7-November-2022]

• Fixes #71 reported by @fetyj, which highlights that antismash module was failing when outputs for a sample were empty.
  • To solve this issue, the module was updated as such the antismash main results is now optional instead of being required, and 'gff conversion' steps are done only when it's results are not empty.
  • PR: #72

fmalmeida/bacannot v3.1.5

Release notes

v3.1.5 [17-September-2022]

• Fixes #64 reported by @fmalmeida, which highlights that the resfinder annotation were sometimes being duplicated because a single gene had intersection to more then one CDS regions, but, only one being "true".
  • To solve such issue, intersections are now sorted by length, and only the first occurence (per gene) is kept.
• As reported in issue #39, named outputs are now used in modules for better readability.

fmalmeida/bacannot v3.1.4

Release notes

v3.1.4 [13-September-2022]

• Fixes #62 reported by @rujinlong, where Island-Path tool was failling because it was running on genbank files with no true CDS. This was hapenning because Bakta writes in the comments that the GBK has 0 CDS and, at first, the module was selecting GBK by checking if the CDS string was there. It has now been modified to also work with Bakta.

fmalmeida/bacannot v3.1.3

Release notes

v3.1.3 [9-September-2022]

Main changes:

• Hmmer version has been fixed in docker image to allow usage of PGAP HMM on prokka annotation
• Bakta has been added as an option instead of prokka, if desired. Bakta database has to been downloaded manually.
• All the annotation summarisation and reporting modules have been updated to understand when users use Prokka or Bakta.