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Before we were checkking if the parent folder is a base minknow data directory by checking if certain folders exist. This created problems when people copied out the folder to a different place. Now we check if the folder is a minknow experiment or if it contains minknow experiments, which should be more reliable
JasonAHendry
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JasonAHendry
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This looks like a good idea and am approving, but had some superficial comments you might look at. In general, I was wondering if we should just be carefully looking for what we need to run Nomadic rather than checking for additional folders that are not used? But could be convinced otherwise.
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| def is_minknow_experiment_dir(path: Path) -> bool: | ||
| expected_folders = {"pod5", "fastq_pass", "fastq_fail"} |
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Thinking about this a bit more, I wonder if for the purposes of Nomadic we really should just be checking for fastq_pass, because that is necessary and sufficient for Nomadic to run?
But I haven't thought carefully enough about it, also e.g. with respect to the waiting period after the run starts and before the folder is generated by MinKNOW.
I think this is also fine, but I guess it introduces unnecessary checks (e.g. pod5, fastq_fail) and also allows proceeding in the absence of fastq_pass.
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Yes, my idea was that we rather want the checks less strict, as this is just a help for the user if they select the wrong folder we can show them this is not a minknow folder, but we rather want to too lose than too strict. I had the checks to strict in the past which was annoying when you actually gave it the right folder, but the check would fail.
So yeah here we are checking for any of those folders just in case for whatever reason fastq_pass was maybe not created yet. Could be that just checking for fastq_pass would be better.
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Before we were checkking if the parent folder is a base minknow data directory by checking if certain folders exist. This created problems when people copied out the folder to a different place. Now we check if the folder is a minknow experiment or if it contains minknow experiments, which should be more reliable