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Eco-Flow / pollen-metabarcoding

A pipeline developled in collaboration with Exeter University
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Cleaning Fastqs Module #1

Closed SimonDMurray closed 3 months ago

SimonDMurray commented 4 months ago

Try to use cutadapt nf-core module but if that does not work then use the biopieces software suite

SimonDMurray commented 4 months ago

I installed and trialled cutadapt however it does not like the singular merged fastq. I will try to now build a biopieces module and see if that works

SimonDMurray commented 3 months ago

Building the biopieces module is incredibly difficult due to the software being released in 2016. So I reworked the logic of the pipeline so that cutadapt trims the individual fastqs first before they are merged by pearRM