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jhuapl-bio / taxtriage

TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomic NGS data. This flexible tool was developed with various use-cases of mNGS in mind.
MIT License
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There are log of warning and channel.view() lines that get printed to the screen while running. #44

Closed erinyoung closed 9 months ago

erinyoung commented 9 months ago

Description of the bug

Kelly asked me to try this workflow on some metagenomic samples that we recently sequenced. The test ran okay, but it seems there are several *.view() statements and other irregularities that get printed to the screen.

Also, I'm unsure what usage to use. I currently have something running, but I thought I would share one of the warning messages that gets printed to the screen.

Command used and terminal output

WARN: Access to undefined parameter `skip_assembly` -- Initialise it to a default value eg. `params.skip_assembly = some_value`

Relevant files

No response

System information

No response

erinyoung commented 9 months ago

Same issue as https://github.com/jhuapl-bio/taxtriage/issues/45