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connor-lab / ncov2019-artic-nf

A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019
GNU Affero General Public License v3.0
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Check for `nanoporeBarcodeDirs` doesn't work for S3 path #36

Open lch14forever opened 4 years ago

lch14forever commented 4 years ago

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!

m-bull commented 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?

lch14forever commented 4 years ago

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

lch14forever commented 4 years ago

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)