Improvements from reviewer's feedback

[matinnuhamunada]

Hi @OmkarSaMo, here is a to-do list based on the reviewer's feedback on the initial manuscript:

Installation

• Mention pre-requisites: gcc, conda or mamba, optional java
• Explicitly mention setting conda to flexible in README.md
• Explicitly mention that it is only tested in Linux (Ubuntu 22.0) not Mac and Windows in README.md
• Built integration test to make sure all environments can be built: snakemake --use-conda --envs-only
• Release on pip or build a conda recipe (later). Maybe focus on pip for now. Test already started in https://test.pypi.org/project/bgcflow-wrapper/
• Check back compatibility between antiSMASH 7 and 6, should be resolved already.

Functionalities

• Build a wildcard to track antiSMASH version in the report metadata and notebooks
• Improve report structure using sub-categories
• Add a python CLI for generating report under build

bgcflow build [database / report] --project [all / project name] #; if error should list available projects

• Add a python CLI for --snakefile with --subworkflow , default return a list of available snakefiles: bgcflow --subworkflow # default return a list of available snakefiles
• BGCFlow serve should list an option of available projects and instructions to build the report.

bgcflow serve [report / metabase / panoptes] # if report then --project flag should be used

• metabase is an illegal project name
• Wrapper to snakemake --until and --unlock
• Make bgcflow init to copy not just point out pep file in the example folder
• Use new snakemake feature to avoid local paths in snakedeploy. See https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#accessing-auxiliary-source-files

Reports

Improve automated reports:

• Prokka
• Roary

Documentation

BGCFlow Wrapper

• Extensive documentation on serve command
• Extensive documentation on build command

Tutorial

• Update tutorial using the lactobacillus delbrueckii: https://github.com/NBChub/bgcflow_tutorial
• Demo report in Zenodo, check compatibility (low priority)
• Add video instructions (low priority)
• Tutorial sections:
  • Introduction (How do I run BGCflow on my computer?)
  • Project structure (How do I set my BGCflow project?)
  • Project setting and rules (How do I set which rules to run?)
  • Running jobs and monitoring (How should I run jobs?)
    • Job errors
    • Reading logs
  • Data structure and output (Where can I find the analysis result of my run?)
  • Building a report and database (How to generate the default reports?)
  • Serving a report
  • Serving metabase and using it (How to read bgcflow database report in metabase)
  • Advanced tutorial - data analysis
    • How to use the subworkflows
    • How to use the network analysis output in cytoscape (Saccharopolyspora example)