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theiagen / public_health_bioinformatics

Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health concern.
GNU General Public License v3.0
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Set phred to 33 on trimmomatic task #332

Closed cimendes closed 4 months ago

cimendes commented 5 months ago

:cool:

Avoiding heartache and keyboard smashing on why trimmomatic is setting everything to the wrong phred encoding!

kapsakcj commented 5 months ago

agreed. Here's how I always run theiaprok_illumina_PE to avoid these trimmomatic errors. Should apply to TheiaCov workflows as well: image

The exact string is "-phred33"

I think this could be a task-level default as it should be applied everywhere. As opposed to a workflow-level default (for example in the read_QC_trim subworkflows