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pha4ge / pipeline-resources

Bioinformatics Pipeline and Visualization resources
https://pha4ge.org/bioinformatics-pipelines-and-visualization/
Apache License 2.0
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Focus Shift to Pipelines Best Practices #34

Closed kevinlibuit closed 3 months ago

kevinlibuit commented 4 months ago

This PR aims to shift the guidance document focus from proposed standards for bioinformatics software to best practices for bioinformatics pipelines. This shift in focus helps to highlight recommendations for the specific type of software that public health labs are having challenges with implementing for pathogen genomics, i.e. bioinformatics workflows; the shift from proposed standards to best practices aims to reflect the evolving nature of these technologies and encourage continuous flexibility, consensus building, and more rapid adoption throughout the community.

The changes to this document include:

  1. Shift in language from Proposed Standards to Best Practices
  2. Narrowed scope from bioinformatics software to bioinformatics pipelines a. Language was added in the Overview section to define this subcategory of bioinformatics software
  3. Removal of Software Security and Vulnerabilities section (refer to #33 for rationale)
  4. Adding of Workflow Management System -- a best practice specific to bioinformatics pipelines
  5. Reorganization into 10 Best Practices with "Pipeline Documentation" encompassing several documentation practices:
  6. Publicly-Accessible Repository
  7. Open-Source License
  8. Version Controlled Software
  9. Workflow Management System
  10. Containerized/Packaged Software
  11. Common File Formats
  12. Software Testing
  13. Benchmark/Validation Datasets
  14. Reference Data Requirements
  15. Pipeline Documentation 10a. Statement of Need with Respect to Public Health Pathogen Genomics 10b. Pipeline Functionality 10c. Contribution, Authorship, and Verified Point of Contact 10d. Conflict of Interest Statement 10e. Community Guidelines for Contribution and Support 10f. Documentation for Local Installation and/or Remote Access (e.g. Web Server or Galaxy/Terra Workflow) 10g. Example Usage
kevinlibuit commented 4 months ago

Updated the Pipeline Documentation practice to include Pipeline Maintenance Statement. I've also reordered this section as follows: 

10. Pipeline Documentation
    10a. Contribution, Authorship, and Verified Point of Contact
    10b. Conflict of Interest Statement
    10c. Pipeline Maintenance
    10d. Community Guidelines for Contribution and Support
    10e. Statement of Need with Respect to Public Health Pathogen Genomics
    10f. Pipeline Functionality
    10g. Documentation for Local Installation and/or Remote Access (e.g. Web Server or Galaxy/Terra Workflow)
    10h. Example Usage