Open lch14forever opened 4 years ago
Hi @lch14forever - apologies for taking a while to get to this. Please could you test https://github.com/connor-lab/ncov2019-artic-nf/commit/d31e8efe07ea3815dc42cac89d823350cff0fdad and see if it fixes your problem?
Wow. That's a brilliant fix! I will try it out and let you know.
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)
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:
https://github.com/connor-lab/ncov2019-artic-nf/blob/39bd87174c1dab67efdb898d066ed616d486d42f/main.nf#L76
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!