samplesheet contains invalid column flow_cell_id

[timternetnet]

Issue Report

Please describe the issue:

When running dorado basecaller, it complains about a column which should be there.

Steps to reproduce the issue:

Samplesheet has the following format:

flow_cell_id,kit,sample_id,experiment_id,barcode,alias
FAXxxxxx,SQK-NBD114-96,XXX,240306_AMP_XXX,barcode01,VLIZ01

Run environment:

• Dorado version: 0.5.1
• Dorado command: dorado basecaller sup 00_raw --barcode-both-ends --kit-name SQK-NBD114-96 --sample-sheet 01_basecalling/16SNanoporeSampleList.csv > 01_basecalling/calls.bam
• Operating system: RHEL8
• Hardware (CPUs, Memory, GPUs): plenty, without a sample sheet it works fine, it's a HPC
• Source data type: pod5
• Source data location (on device or networked drive - NFS, etc.): on device

Logs

Output:

Sample sheet contains invalid column flow_cell_id

Any pointers? :)

[HalfPhoton]

@timternetnet, Can you explain what's complaining specifically? Do you have an error message? Does your sample sheet meet the specifications SampleSheets.md? Kind regards, Rich

[timternetnet]

Dear @HalfPhoton , I didn't see anything obvious wrong with my samplesheet, but now trying to prove what went wrong it seems to work when I reduce the sample sheet to a couple of lines (I had 96 samples). So I'll test further and try to track down why it didn't work the first time around, perhaps I missed a weird character somewhere.

Thanks for getting back to me! I'll close this one for now.