v2024.3.0 MinKNOW 6.0 compatibilty, pass reads and bug fixes

[Adoni5]

What's new

The highlights:

• Updated to use MinKNOW >= 6.0 🥳 There were some minknow_api endpoint changes, around the basecaller version. Big one is the switch from using read_id to read_number, and new strand classifications.

Warning

Breaking for any version of MinKNOW <= 6.0.0
As of readfish >=2024.3.0 we no longer support guppy.

• Uses py_basecall_client.pass_reads to send reads to the base caller for improved performance.
• Bug fixes, most are for the flongle, due to the final column of pores being 6 channels not 10, like the preceding columns.
• Chores - updated to use Node 20 actions which was surprisingly easy over all

What's Changed

• Feature/minknow-6-compatibilyt by @Adoni5 in Detect native adaptive sampling and warrn. #368
• Feature/pass reads by @Adoni5 in Feature/pass reads #361
• Delete dc918797-33da-4414-9999-eb9132d22971_readfish.tsv by @Adoni5 in Delete dc918797-33da-4414-9999-eb9132d22971_readfish.tsv #380
• Catch some "placeholder" channel positions being 0 on flongle by @Adoni5 in Catch some "placeholder" channel positions being 0 on flongle #384
• Fix issue340 - live TOML handling by @Adoni5 in Fix issue340 - live TOML handling #383
• bump all node 16 actions to node 20 by @Adoni5 in bump all node 16 actions to node 20 #377
• Minor change to readme to better reflect update to 6.0 and deprecatio… by @mattloose in https://github.com/LooseLab/readfish/pull/

Full Changelog: 2024.2.0...v2024.3.0

🙏🏼 for Rory's thesis

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This discussion was created from the release v2024.3.0 MinKNOW 6.0 compatibilty, pass reads and bug fixes.