Falco v2.0

[andrewdavidsmith]

Discussion related to falco2, aimed to release in July August 2026.

Example topics here:

-- Any questions
-- Feature requests
-- Tell me what kinds of changes would be deal-breakers

Note:
-- Motivation for changes: open up opportunities for future performance increases and incorporate preseq stats
-- This post will be edited soon with a summary of anticipated changes to the user interface and behaviors
-- Falco v1.X will be maintained for some time alongside v2.0, and I will accept bug reports on v1.X in case you can't migrate

[andrewdavidsmith]

Notes

(Notes to self for preparing docs)

• The falco source was rewritten 100% for v2.0, every line.
• This means there will be more bugs.
• I plan to release patches frequently as bugs are identified.
• A major version (e.g., v2.0) involves breaking changes. Everything might break, from the interface to the outputs. This is important if you use falco in a pipeline.
• I aimed to not break the output file formats so that downstream parsing the fastqc_restults.txt and summary.txt files should still parse the same way.
• The command line interface is totally different, and much more concise.
• The config file format is identical.
• If you are building falco v2.0 from source, there are more dependencies and I moved to cmake.
• I plan to maintain binaries aimed to work on any macOS or Linux system without needing to install anything else.
• There are 3 different kinds of analyses where the numbers in the output will not be identical. I will explain these separately.