dorado basecaller has duplicate command line flag -o

[lucast122]

Issue Report

Please describe the issue:

dorado basecaller uses the flag -o twice once for output folder and once for overlap. Output folder can only be defined using --output-dir though.

Please provide a clear and concise description of the issue you are seeing and the result you expect.

dorado basecaller -o sample/ dna_r10.4.1_e8.2_400bps_fast@v5.0.0 . gives [2024-09-25 15:03:12.156] [error] Failed to parse 'a' as decimal integer: pattern 'a' not found

Steps to reproduce the issue:

Please list any steps to reproduce the issue.

Run environment:

• Dorado version: 0.8.0+acec121
• Dorado command: dorado basecaller -o a dna_r10.4.1_e8.2_400bps_fast@v5.0.0 .
• Operating system: Ubuntu20
• Hardware (CPUs, Memory, GPUs): ryzen threadripper, 512GB RAM, NVIDIA RTX3070Ti
• Source data type (e.g., pod5 or fast5 - please note we always recommend converting to pod5 for optimal basecalling performance): pod5
• Source data location (on device or networked drive - NFS, etc.): device
• Details about data (flow cell, kit, read lengths, number of reads, total dataset size in MB/GB/TB):
• Dataset to reproduce, if applicable (small subset of data to share as a pod5 to reproduce the issue):

Logs

• Please provide output trace of dorado (run dorado with -v, or -vv on a small subset)

[HalfPhoton]

@lucast122 , thanks for raising this issue. We'll get this fixed.

Best regards, Rich