fmalmeida/bacannot v2.3.2

The pipeline

bacannot, is a customisable, easy to use, pipeline that uses state-of-the-art software for comprehensively annotating prokaryotic genomes having only Docker and Nextflow as dependencies. It is able to annotate and detect virulence and resistance genes, plasmids, genomic islands, prophages, ICEs, KO, and more.

Release notes

1. There is a smal fix in the update_database_image.sh so it takes only the first two numbers of release tags.
2. Changed the pipeline to now accept the resfinder species panel "Other"
3. Fixed the Resfinder report to understand when only the pointfinder mutations are empty.

fmalmeida/bacannot v2.3.1

The pipeline

bacannot, is a customisable, easy to use, pipeline that uses state-of-the-art software for comprehensively annotating prokaryotic genomes having only Docker and Nextflow as dependencies. It is able to annotate and detect virulence and resistance genes, plasmids, genomic islands, prophages, ICEs, KO, and more.

Release notes

Fix in main.nf

Fixed a very small problem that was holding up the execution of flye and unicycler when using the multi-samples workflow with the "samplesheet.yml". The scripts for unicycler and flye under multi-samples workflow was with an "if" statement in the wrong position.

fmalmeida/bacannot v2.3

The pipeline

bacannot, is a customisable, easy to use, pipeline that uses state-of-the-art software for comprehensively annotating prokaryotic genomes having only Docker and Nextflow as dependencies. It is able to annotate and detect virulence and resistance genes, plasmids, genomic islands, prophages, ICEs, KO, and more.

Release notes

v2.3

• Dockerfile
  • The dockerfile structure has changed and its size reduced
  • started to track the main tools and databases with dockerfile release tags
  • Github actions wer set to update the main dockerfile containing the databases every month
  • Users can now easily update the databases in the docker image at any time
• New modules
  • A module for identification of top 10 closest Refseq genomes has been added with RefSeq Masher
  • A module for focused detection of insertion sequences has been added with digIS
  • A new report has been added to summarise the most general annotation results
• Small fixes
  • The image generated by the vfdb virulence report has been fixed
  • Examples of outputs have been added to the documentation
  • Barrnap is now properly outputting its version

fmalmeida/bacannot v2.2

The pipeline

bacannot, is a customisable, easy to use, pipeline that uses state-of-the-art software for comprehensively annotating prokaryotic genomes having only Docker and Nextflow as dependencies. It is able to annotate and detect virulence and resistance genes, plasmids, genomic islands, prophages, ICEs, KO, and more.

fmalmeida/bacannot v2.1

The pipeline

bacannot, is a customisable, easy to use, pipeline that uses state-of-the-art software for comprehensively annotating prokaryotic genomes having only Docker and Nextflow as dependencies. It is able to annotate and detect virulence and resistance genes, plasmids, genomic islands, prophages, ICEs, KO, and more.

fmalmeida/bacannot v2.0

Changes

This release marks the change from nextflow DSL 1 to DSL 2. Also it has a lot of minor changes such as database headers configuration, parameters syntax changes and HTML reports updates in order to understand these changes.

The main workflow does not have huge alterations, the only ones are:

• Output prefix is set based on input filename
• KEGGDecoder has been added
• ARGminer has been added
• Scan of full-length ICEs has been added
• SQLdb has been removed in order to integrate mongoDB (in next releases)
• Roary has been removed (we will create a different workflow in order to execute the pangenome analysis separately)