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@etal etal released this 02 Mar 03:55
· 216 commits to main since this release
v2.1
a92a6e0

This release revamps the output report and improves several aspects of portability. Script usage is similar to previous releases.

Report updates

  • A new script create_report.R, intended to replace plotAAVreport.R, generates equivalent reports in both HTML and PDF format from the same Rmarkdown source. Command-line usage of create_report.R is the same as plotAAVreport.R, and it should function as a drop-in replacement. (#3)
  • The updated report includes new plots, tables, and explanatory text regarding AAV types, subtypes, and flip/flop configurations. (#3, #5)

Portability

  • Docker: the scripts and dependencies are captured in a Dockerfile that can be used to build portable containers. (#1)
  • Automated testing: a simple CI suite now runs on each PR via GitHub Actions to verify the code under Python 3.8, 3.9, and 3.10. (#1)
  • MIT license: the codebase is now formally available as open-source software under a permissive, OSI-compatible MIT license. Previously, the permissible use was not stated explicitly. (#2)
  • Semi-manual testing: a new test/Makefile can be run manually to pull in public PacBio example datasets and run this repo's scripts on them to perform the analysis and produce reports. (#3)
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