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`[error] Unknown argument: --kit-name` when combining --duplex with --barcode_kit SQK-NBD114-96 #42

Open chris-krohn opened 4 months ago

chris-krohn commented 4 months ago

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/dna_r10.4.1_e8.2_400bps_sup@v5.0.0" "." "--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 dna_r10.4.1_e8.2_400bps_sup@v5.0.0 \ --barcode_kit SQK-NBD114-96\ --duplex

RenzoTale88 commented 4 months ago

@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.