Check for nanoporeBarcodeDirs doesn't work for S3 path

[lch14forever]

Hi,

Thanks for developing this convenient pipeline. I am trying to run this on AWS batch but I found some problem in detecting the barcode option. Specifically I think this line only works for a local path:

ncov2019-artic-nf/main.nf

Line 76 in 39bd871

def nanoporeBarcodeDirs = new FileNameByRegexFinder().getFileNames(params.basecalled_fastq, /.*barcode[0-9]{1,4}$/)

Do you have any suggestions? The only thing I can come up with is to add a flag param to let user specify whether barcodes were used.

Thanks in advance!

[m-bull]

Hi @lch14forever - apologies for taking a while to get to this. Please could you test d31e8ef and see if it fixes your problem?

[lch14forever]

Wow. That's a brilliant fix! I will try it out and let you know.

[lch14forever]

Hi,

I think maybe the line for checking non-barcoded run should include compressed fastqs?

nanoporeNoBarcode = file("${params.basecalled_fastq}/*.fastq*", type: 'file', maxdepth: 1)