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nanoporetech / minknow_api

Protobuf and gRPC specifications for the MinKNOW API
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The FAST5 is not dumped until I turn ON basecalling #5

Closed harisankarsadasivan closed 4 years ago

harisankarsadasivan commented 4 years ago

WHen i sequence using the start and stop protocols via python, i do not see any FAST5's being dumped. But, when I navigate to the GUI and turn on basecalling, the FAST5's appear. How do I see the FAST5's when I run using python interface? @iiSeymour @jorj1988

0x55555555 commented 4 years ago

Hello,

the start_protocol request expects an args parameter: https://github.com/nanoporetech/minknow_api/blob/master/minknow/rpc/protocol.proto#L135, which can be used to configure the script.

In order to turn on fast5, set args to [ "--fast5=on", "--fast5_data trace_table fastq raw" ]

The call can also configure other common settings, for example:

We are looking to improve the protocol start/setup interface in a future release - that will make a these settings clearer for users of the api.