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.

fmalmeida/bacannot v3.1.2

Release notes

This version contains:

• A fix on the custom blast report file which had an wrong ifelse statement definition
• Updated version of renv docker with fixed report Rmd
• Addition of checkIfExists statements when loading file to make sure that user is pointing to files that exists and did not misspelled them
• Fixed a small misspelling on example samplesheet url
• A small fix on phigaro.nf module which was causing the pipeline to fail when its outputs were empty

Thanks to @fetyj for spotting these issues.

fmalmeida/bacannot v3.1.1

Release notes

This version contains a quick fix spotted by @fetyj described in issue #52. Now the path to the argminer backup database is given as full path.

fmalmeida/bacannot v3.1

Release notes

In this version of the pipeline, N things have been added / changed:

1. In order to diminish docker image sizes and to avoid problems with its download hanging and being limited, the databases are not anymore available inside the images. Users must first download the databases with the parameter --get_dbs.
   • See https://bacannot.readthedocs.io/en/master/quickstart/#bacannot-databases
2. Since the databases are now downloaded by the pipeline and saved in the user machine, the pipeline now requires the database path as input. E.g. --bacannot_db ./bacannot_dbs.
   • See https://bacannot.readthedocs.io/en/master/quickstart/#run-the-pipeline
3. The pipeline now does not have a default profile set, and users must use either -profile docker or -profile singularity, otherwise it will try to load tools from your system and will surely fail.
4. In previous versions, the pipeline only accepted custom gene databases for additional annotation in nucleotide fasta. Now, the pipeline also accepts protein fastas. Be aware that headers must be properly formatted. Additionally, the pipeline now also accepts a list of NCBI protein IDs as additional database with --ncbi_proteins. Using it, the pipeline will download the protein sequences and format the databases automatically.
   • See https://bacannot.readthedocs.io/en/master/custom-db/
5. Finally, the pipeline have been reestructured to use and benefit more from the incredible nf-core framework.

fmalmeida/bacannot v3.0.1

Release notes

additions

In this version of the pipeline, two things have been added:

1. A small dataset with Haemophilus influenzae to provide a quicktest profile that runs in 10~20 min.
2. A new github action to test the upcoming changes for each new PR using this available quicktest.

fixes/changes/improvements

These improvements in the code and standardization of namings throughout the pipeline have been made possible thanks to the awesome contributions from @abhi18av

1. The config files have been splitout into smaller ones and placed inside a conf directory to keep things more organized (PR #43)
2. The names of channels and modules in the pipeline have been changed so they are more standardized and more similar to how it is used for nextflow pipelines in general, so it is easier to read and understand (PR #45)

comments

Nothing has changed in terms of how tools are called and used, thus the docker image still the same. In fact, patch/fix releases (x.x.x) will always use the docker from breaking/features release (x.x)

fmalmeida/bacannot v3.0

Release notes

input configuration

• In order to keeps things the least complex possible and to make the pipeline less confusing, the pipeline has been reconfigured in order to properly use it, in all workflow types (for multiple samples at once or just one) through the samplesheet.
  • Because of that, we removed the possibility to pass the input reads via the command line and now, the files input data files, must always be set inside the samplesheet, even if analysing only one sample.
  • Read more at: https://bacannot.readthedocs.io/en/latest/samplesheet.html
  • Check the template samplesheet at: https://github.com/fmalmeida/bacannot/blob/master/example_samplesheet.yaml
  • The samplesheet is given with the parameter --input
• Due to the implementation above, the folowing parameters are now deprecated, since they are now set inside the YAML file:
  • --genome
  • --sreads_paired
  • --sreads_single
  • --lreads
  • --lreads_type
  • --nanopolish_fast5
  • --nanopolish_fastq
• The --resfinder_species parameter keeps existing. It now sets a default for all samples in the samplesheet. However, when a sample has another value for that set with the key resfinder, the pipeline will use, for that specific sample, the value found inside the samplesheet.

nomenclature change

• In order to make it simple and natural, two changes ocurred in input/output parameters
  • The --outdir parameter is now --output
  • The --in_yaml parameter is now --input

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