How to use the extra args?

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Assessment

Difficulty
2/5
Estimated time
1-3 hours
Newbie friendliness
35/100
Issue type
Documentation
Clarity
Mostly clear
Activity status
Stale
Tech stack
python
Domain
api

Research direction

Start at the protocol_args.extend(args) entry point and compare it with the documented fast5_out option. Confirm the accepted argument form with a minimal invocation or existing tests, then update the relevant usage documentation or example so including fastq and the trace table is unambiguous.

Written by the indexing model from the issue text.

Description

My requirement is to make fast5 include fastq and trace table. By looking up the instructions, I understand that the fast5_out should be set out to True. Which of the following expression is correct in syntax?

extra_args=["--fast5_out=True"]
extra_args=["fast5_out=True"]
extra_args=["fast5_out=on"]
extra_args=["--fast5_out=on"]
extra_args=["--fast5_out"]

extra_args would be passed to protocol_args.extend(args).

I have failed many times . I would appreciate your help.

Dominant language
Python
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