Nanoq on multiple compressed fastq.gz files

[RommerskirchenA]

Hi,

I encounter an error when running nanoq on multiple fastq.gz files (from one barcode) with their generic Nanopore names, it usually tells me that file *_10.fastq.gz isn't valid in this context. When first concatinating the file this error is not raised.

error: Found argument 'barcode13/PAQ96126_pass_barcode13_a9873f14_18d6854d_10.fastq.gz' which wasn't expected, or isn't valid in this context

Is there a way to circumvent this?

Thanks in advance!

[esteinig]

@RommerskirchenA could you list the command you ran for this precisely?

[RommerskirchenA]

yes sure:

nanoq -i path/to/barcodes/*.fastq.gz -q 18 > path/to/filtered_reads.fastq.gz

[esteinig]

Nanoq does not take multiple --input parameters. You can pipe find output into nanoq though, have a look here:

https://github.com/esteinig/nanoq?tab=readme-ov-file#online-runs