[bug] Bactopia doesn't like uncompressed FASTQs from ONT

[fanninpm]

Description
I was trying out Bactopia with some uncompressed FASTQs from ONT, when the run crashed during the gathering stage. It seems like Bactopia is assuming that ONT reads are properly gzip'd.

Steps to Reproduce
Steps to reproduce the behavior:

bactopia --sample my_sample --ont my_sample.fastq

Expected Behavior
Bactopia should detect that this file is uncompressed and proceed as normal.

Execution Environment

• Bactopia Version: bactopia 3.0.1
• OS: Debian 12
• Environment: Google Batch (it shouldn't matter for the purposes of this bug report)

Additional Information
I can't easily gzip the input files in situ, as I specify my inputs from a Google Cloud bucket.

[rpetit3]

Hi @fanninpm

You will need to compress the input FASTQs. The requirement for compressed FASTQs is a practice shared by Bactopia and nf-core.

Cheers,
Robert