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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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Error running articGuppyplex #31

Closed sthifx closed 4 years ago

sthifx commented 4 years ago

When running the latest version on our nanopore data, I'm getting the following error:

File "PATH/lib/python3.6/site-packages/artic/pipeline.py", line 35, in run_subtool submodule.run(parser, args) File "PATH/python3.6/site-packages/artic/guppyplex.py", line 36, in run fastqoutfn = "%s%s.fastq" % (args.prefix, os.path.basename(barcode_directory)) NameError: name 'barcode_directory' is not defined

It looks like barcode_directory is never instantiated in guppyplex.py

The offending command from the nextflow work directory in .command.sh is

artic guppyplex --min-length 400 --max-length 700 --prefix PREFIX --directory barcode04

Apologies if this is me being daft, and thanks in advance!

m-bull commented 4 years ago

Sorry about that, not you being daft at all! A product of everything moving very quickly at the moment, and it looks like ARTIC broke something on the master branch of the fieldbioinformatics repo. This workflow probably shouldn't use the master branch from there anyway!

I've pinned the commit id of fieldbioinformatics in https://github.com/connor-lab/ncov2019-artic-nf/commit/dd5cb0603b56ba61feb11222e4acd9fe9630c846 - this works fine in my hands. Please update your containers if you've made any. Conda should work fine just using https://github.com/connor-lab/ncov2019-artic-nf/commit/dd5cb0603b56ba61feb11222e4acd9fe9630c846.

sthifx commented 4 years ago

Thanks Matt, and thanks for the v fast response! Seems to be working great now.

All the best, Sam