Release Notes

v3.4.3 [26-November-2025]

• [[#136]]
  • Corrects syntax of optional tuplws for Nextflow 25.10 compatibility
  • Thanks to @robertpark1228

Release Notes

v3.4.2 [29-March-2025]

• [[#131]]
  • Add a small sed command to correct wrong fasta headers from public databases
• correct zenodo_get command to always download latest
• correct channel parsing for generating html reports of custom databases
• correct description field of run_blasts.py script

Release notes

v3.4.1 [14-November-2024]

• [[#127]]
  • Allow GET_NCBI_MODULE fail to be ignored, and adjust resources
  • Add parameter to skip sourmash workflow
  • Adjust file permissions in module GET_NCBI_MODULE

Release notes

v3.4.0 [07-July-2024]

• [#30]
  • Add sourmash to workflow
• Updated pre-built database in https://zenodo.org/doi/10.5281/zenodo.7615811

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

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.

Release notes

v3.3.1 [29-October-2023]

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

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]

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

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