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nanoporetech / minknow_api

Protobuf and gRPC specifications for the MinKNOW API
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How to have a buik fast5 generated through the MinKNOW API? #29

Closed neuropathbasel closed 2 years ago

neuropathbasel commented 2 years ago

Is there a way to activate the bulk fast5 output through this supplied version of the MinKNOW API? If not (yet) - where would we have to modify the code to have this generated by default? Any feedback would be highly appreciated.

neuropathbasel commented 2 years ago

Just figured out that this can also be done in the /tools/protocols.py script

I have added the following lines above the protocol_args.extend(args) line. This seems to work fine.

    #autogenerate bulk file for every run, added 20210728
    protocol_args.append("--generate_bulk_file=on")
    protocol_args.append("--bulk_file_content")
    protocol_args.append("raw=[[1,512]]")
    protocol_args.append("events=[[1,512]]")
    protocol_args.append("read_table=[[1,512]]")

    protocol_args.extend(args)

I am closing this issue.