jhayer/baargin

Issues

• There are no automated tests that let me verify the functionality

  #47 opened a year ago by jhayer
  2

• [JOSS] @mberacochea's feedback for the JOSS submission

  #26 opened a year ago by mberacochea
  5

• There are no automated tests. My recommendation is to use like nf-test or pytest-workflow. By doing this, the functionality of the pipeline can be easily tested. This introduces some extra work, so I would recommend adding at least one nf-test or pytest-worklow test for the whole pipeline. If this is not feasible, please provide some documentation around the test data set included in the repo, specially around the output files. Which output files are the key ones, and how should they look like.

  #48 opened a year ago by jhayer
  1

• [JOSS] @rcannood's feedback for the JOSS submission

  #13 opened a year ago by rcannood
  5

• Please create a release of Baargin on GitHub, so users can run baargin using the command:

  #44 opened a year ago by jhayer
  1

• Ideally the only required software to run the pipeline should be Nextflow and Docker/Singularity. I would suggest review the installation instructions, requiring a conda env. shouldn't be required.

  #36 opened a year ago by jhayer
  2

• A nice UX pattern is to have the download_dbs.py to be part of the pipeline itself. It's possible to have a module to download the dbs, if they are missing. This lowers the entry barrier in my experience.

  #41 opened a year ago by jhayer
  1

• There are no community guidelines.

  #28 opened a year ago by jhayer
  0

• It would be useful to have a bit of more information in the README.

  #27 opened a year ago by jhayer
  0

• This is linked to my previuos comment in the "Functionality" entry. Nextflow + Singularity/Docker should be the only requirements to run the pipeline

  #37 opened a year ago by jhayer
  0

• I recommend to remove unused-commented code and unused modules (such as https://github.com/jhayer/baargin/blob/main/modules/emblmygff3.nf)

  #32 opened a year ago by jhayer
  0

• This is missing from the software paper

  #30 opened a year ago by jhayer
  0

• Typo: "Hight" → "High"

  #18 opened a year ago by jhayer
  0

• Python: for tabular results it's recommended to use the stdlib csv module. This makes the code easier to follow as the csv module is responsable for the formatting. Example -> https://github.com/jhayer/baargin/blob/main/bin/amrfinder_compile_heatmap.py#L79

  #45 opened a year ago by jhayer
  0

• The containers.config file should not have the cpus, memory and time limits for the modules. Placing those in a base.config or similar makes it easier to find the module's resource requirements.

  #42 opened a year ago by jhayer
  0

• The params are available in the modules, there is no need to provide that on import (such as: `include {quast} from './modules/quast.nf' params(output: params.output)`

  #38 opened a year ago by jhayer
  0

• There are some nextflow modules with strange identation, such as https://github.com/jhayer/baargin/blob/main/modules/agat.nf

  #31 opened a year ago by jhayer
  0

• There are no guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

  #24 opened a year ago by jhayer
  0

• Please provide a more structured documentation of the parameters. The current descriptions contains textual instructions, an example nextflow params file, and the output of the nextflow params file.

  #21 opened a year ago by jhayer
  0

• As mentioned earlier, please provide clear instructions on which steps need to be performed to run the pipeline. The only requirements should be Nextflow and (Docker or Singularity). I don't understand why the installation packages currently instruct me to set up a Conda environment or install Python packages.

  #35 opened a year ago by jhayer
  0

• Please review the installation instructions. I shouldn't need to install a conda environment to be able to run a Nextflow pipeline.

  #34 opened a year ago by jhayer
  0

• Assuming that the pipeline documentation is the README.md in the root of the repo, I didn't find a statement of need

  #19 opened a year ago by jhayer
  0

• There is no section which compares Baargin to other commonly-used packages

  #29 opened a year ago by jhayer
  0

• The sentences in the paragraph "Statement of Need" contain two or three different messages which you try to convey at the same time. This causes the sentences in this paragraph to become quite long and hard to read. Can you rephrase this section to make it less wordy?

  #16 opened a year ago by jhayer
  0

• It might be better to rephrase "it is now affordable to sequence the full genomes of hundreds of bacterial strains at a time" as "it has become more affordable to sequence the full genomes of hundreds of bacterial strains at a time."

  #14 opened a year ago by jhayer
  0

• MicrobeAnnotator - We could add this tool to improve functional annotation

  #1 opened 2 years ago by Juke34
  1

• AMRFinder DB auto update

  #12 opened 2 years ago by jhayer
  0

• Add download of mini_kraken_db to the download_db script

  #8 opened 2 years ago by jhayer
  0

• Prepare conda env for local run

  #9 opened 2 years ago by jhayer
  0

• Test path input before running

  #7 opened 2 years ago by jhayer
  2

• Pre-download of mandatory DBs

  #3 opened 2 years ago by jhayer
  1

• Pre-install of KrakenTools

  #4 opened 2 years ago by jhayer
  0