promethion ready - checklist

[WardDeb]

Todo's to make the workflow 'promethion ready'. Related to #138, #139, #140

• merge basecalled bam files (e.g. basecalled output)
• fetch exact dorado (server) version + model used in MinKNOW and store this in the config / metadata to ship to end user. For MinKNOW v 23.07.12 the information in the json is confusing (e.g. guppy flags while dorado is used), the info in html should be correct.
• basecalled bam files generated with minKNOW are not compatible with dorado align (v0.4.1 & 0.5.0).
• basecalled bam files generated with minKNOW are not compatible with modbam2bed.
• model_def & model are confusing in the metadata yaml (HAC vs SUP)

[WardDeb]

per on site meeting:

• parameters should be parsed from sequencingrun.html files rather then json/md
• important to discriminate between minKNOW version/models & dorado models
• bam header information should be parsed for consistency
• explore expansion on epi2me's basecalling workflow for implementation into minKNOW