fmalmeida/bacannot v2.4.2

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

This is a super small fix:

• Now they show information about the sample, not the task, which is more useful for users to track their analysis

fmalmeida/bacannot v2.4.1

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

Super small fix to properly load YAML file when using the pipeline with cloud computing environments such as AWS/S3-bucket:

# from
parameter_yaml = new FileInputStream(new File(params.in_yaml))
# to
parameter_yaml = file(params.in_yaml).readLines().join("\n")

fmalmeida/bacannot v2.4

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

This release marks the incrementation of the pipeline with two more modules:

1. A new module for the annotation of secondary metabolites with antiSMASH has been added.
   • The modules runs only with antiSMASH core modules in order to keep it fast
   • This step can be skipped with --skip_antismash
2. A new plugin has been added to the Web (Shiny) App. SequenceServer has been implemented inside the app so that users can quickly execute and visualise blast alignments against the samples' genome, genes and proteins.

Also, a small fix was performed in the run_jbrowse.sh script. To add the antismash results and to properly check whether digIS results are available or not.

Finally, a small fix in the merge annotation process and SQLparser in the shiny app was also performed to include Resfinder as an option.

Because of that:

• The fmalmeida/bacannot:server has been updated
• A new image fmalmeida/bacannot:antismash is now available for antiSMASH module

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)