[error] Unknown argument: --kit-name when combining --duplex with --barcode_kit SQK-NBD114-96

[chris-krohn]

Ask away!

Running the below workflow options resulted in the following errror.
Command error: [2024-06-29 22:56:13.093] [info] Running: "duplex" "/models/[email protected]" "." "--kit-name" "SQK-NBD114-96" "--device" "cuda:all" [2024-06-29 22:56:13.100] [error] Unknown argument: --kit-name [main_samview] fail to read the header from "-".

nextflow.log

This workflow runs fine without the --barcode_kit SQK-NBD114-96 option. Is that expected behaviour?

Thanks!

Workflow that resulted in above error:
nextflow run epi2me-labs/wf-basecalling \
-profile standard \
--input pod5/ \
--dorado_ext pod5 \
--out_dir output_SUP_duplex \
--basecaller_cfg [email protected] \
--barcode_kit SQK-NBD114-96\
--duplex

[RenzoTale88]

@chrismitbiz apologies for the inconvenience, duplex calling does not support barcoding kit as an option. We will amend this in the next release of the workflow to raise an error when these two options are selected.